Starting phenix.real_space_refine on Wed May 8 05:24:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ufh_42207/05_2024/8ufh_42207_updated.pdb" } resolution = 3.2 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= 0.004 sd= 0.123 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 Cl 1 4.86 5 C 5917 2.51 5 N 1538 2.21 5 O 1630 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 207": "OE1" <-> "OE2" Residue "A GLU 213": "OE1" <-> "OE2" Residue "B GLU 213": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "F GLU 58": "OE1" <-> "OE2" Residue "G GLU 65": "OE1" <-> "OE2" Residue "G GLU 259": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5322/modules/chem_data/mon_lib" Total number of atoms: 9128 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1876 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 6, 'TRANS': 232} Chain: "B" Number of atoms: 1869 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1869 Classifications: {'peptide': 238} Link IDs: {'PTRANS': 6, 'TRANS': 231} Chain: "F" Number of atoms: 2525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2525 Classifications: {'peptide': 316} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 303} Chain breaks: 4 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 2629 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2629 Classifications: {'peptide': 327} Link IDs: {'PTRANS': 11, 'TRANS': 315} Chain breaks: 2 Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 229 Unusual residues: {'WJW': 1, 'Y75': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.97, per 1000 atoms: 0.54 Number of scatterers: 9128 At special positions: 0 Unit cell: (66.825, 107.25, 133.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 40 16.00 P 2 15.00 O 1630 8.00 N 1538 7.00 C 5917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 1.7 seconds 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2078 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 46 helices and 10 sheets defined 52.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.88 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 80 through 86 Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.866A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 removed outlier: 3.511A pdb=" N GLN A 124 " --> pdb=" O GLN A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 138 No H-bonds generated for 'chain 'A' and resid 136 through 138' Processing helix chain 'A' and resid 148 through 161 Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.005A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.674A pdb=" N ALA A 210 " --> pdb=" O ARG A 206 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 234 Processing helix chain 'A' and resid 236 through 241 Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 80 through 86 Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.809A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.725A pdb=" N GLN B 124 " --> pdb=" O GLN B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 136 through 138 No H-bonds generated for 'chain 'B' and resid 136 through 138' Processing helix chain 'B' and resid 148 through 162 removed outlier: 3.851A pdb=" N ALA B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 193 removed outlier: 4.250A pdb=" N GLY B 182 " --> pdb=" O PRO B 178 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N ASP B 183 " --> pdb=" O ILE B 179 " (cutoff:3.500A) Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 229 through 233 Processing helix chain 'B' and resid 236 through 241 Processing helix chain 'F' and resid 3 through 39 removed outlier: 3.518A pdb=" N GLY F 29 " --> pdb=" O ILE F 25 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ARG F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.062A pdb=" N LEU F 62 " --> pdb=" O GLU F 58 " (cutoff:3.500A) Proline residue: F 65 - end of helix Processing helix chain 'F' and resid 84 through 91 Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.567A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ILE F 103 " --> pdb=" O GLY F 99 " (cutoff:3.500A) Proline residue: F 104 - end of helix Processing helix chain 'F' and resid 120 through 135 Processing helix chain 'F' and resid 140 through 143 Processing helix chain 'F' and resid 248 through 250 No H-bonds generated for 'chain 'F' and resid 248 through 250' Processing helix chain 'F' and resid 253 through 256 No H-bonds generated for 'chain 'F' and resid 253 through 256' Processing helix chain 'F' and resid 263 through 274 Processing helix chain 'F' and resid 276 through 284 removed outlier: 3.660A pdb=" N ILE F 279 " --> pdb=" O PRO F 276 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N VAL F 280 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE F 281 " --> pdb=" O THR F 278 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 282 " --> pdb=" O ILE F 279 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N MET F 284 " --> pdb=" O ILE F 281 " (cutoff:3.500A) Processing helix chain 'F' and resid 302 through 324 Processing helix chain 'F' and resid 330 through 349 Proline residue: F 334 - end of helix removed outlier: 3.933A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ILE F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA F 343 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA F 344 " --> pdb=" O GLY F 341 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LEU F 346 " --> pdb=" O ALA F 343 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 41 removed outlier: 4.045A pdb=" N LEU G 36 " --> pdb=" O LEU G 32 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY G 37 " --> pdb=" O PHE G 33 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N SER G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ASN G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 Processing helix chain 'G' and resid 59 through 84 Proline residue: G 68 - end of helix Processing helix chain 'G' and resid 87 through 94 Processing helix chain 'G' and resid 98 through 122 removed outlier: 3.969A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 134 removed outlier: 3.614A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 239 removed outlier: 4.512A pdb=" N HIS G 236 " --> pdb=" O LYS G 233 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR G 239 " --> pdb=" O HIS G 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 242 through 244 No H-bonds generated for 'chain 'G' and resid 242 through 244' Processing helix chain 'G' and resid 247 through 260 Processing helix chain 'G' and resid 265 through 275 Processing helix chain 'G' and resid 277 through 293 Processing helix chain 'G' and resid 301 through 327 removed outlier: 3.569A pdb=" N ASP G 320 " --> pdb=" O TYR G 316 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU G 327 " --> pdb=" O GLY G 323 " (cutoff:3.500A) Processing helix chain 'G' and resid 333 through 353 Proline residue: G 340 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 32 through 35 Processing sheet with id= B, first strand: chain 'A' and resid 222 through 227 removed outlier: 6.607A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N HIS A 214 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N VAL A 198 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU A 42 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 200 " --> pdb=" O LEU A 42 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 17 through 19 removed outlier: 7.516A pdb=" N LYS A 19 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LYS A 28 " --> pdb=" O LYS A 19 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 32 through 35 Processing sheet with id= E, first strand: chain 'B' and resid 222 through 227 removed outlier: 6.810A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL B 198 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LEU B 42 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE B 200 " --> pdb=" O LEU B 42 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 17 through 19 removed outlier: 7.650A pdb=" N LYS B 19 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N LYS B 28 " --> pdb=" O LYS B 19 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'F' and resid 148 through 152 removed outlier: 4.159A pdb=" N GLU F 148 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA F 159 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'F' and resid 192 through 194 Processing sheet with id= I, first strand: chain 'G' and resid 149 through 153 Processing sheet with id= J, first strand: chain 'G' and resid 162 through 164 removed outlier: 3.849A pdb=" N GLN G 168 " --> pdb=" O ASN G 164 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N GLN G 191 " --> pdb=" O ASN G 203 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL G 195 " --> pdb=" O GLN G 199 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N GLN G 199 " --> pdb=" O VAL G 195 " (cutoff:3.500A) 464 hydrogen bonds defined for protein. 1293 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: 2.92 Time building geometry restraints manager: 4.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1476 1.32 - 1.44: 2433 1.44 - 1.56: 5322 1.56 - 1.69: 2 1.69 - 1.81: 75 Bond restraints: 9308 Sorted by residual: bond pdb=" C21 WJW F 401 " pdb=" N20 WJW F 401 " ideal model delta sigma weight residual 1.559 1.335 0.224 2.00e-02 2.50e+03 1.25e+02 bond pdb=" C75 WJW F 401 " pdb=" N74 WJW F 401 " ideal model delta sigma weight residual 1.550 1.335 0.215 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C55 Y75 F 402 " pdb=" N27 Y75 F 402 " ideal model delta sigma weight residual 1.526 1.325 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C16 WJW F 401 " pdb=" O17 WJW F 401 " ideal model delta sigma weight residual 1.502 1.339 0.163 2.00e-02 2.50e+03 6.63e+01 bond pdb=" CI0 WJW F 401 " pdb=" NH9 WJW F 401 " ideal model delta sigma weight residual 1.498 1.337 0.161 2.00e-02 2.50e+03 6.45e+01 ... (remaining 9303 not shown) Histogram of bond angle deviations from ideal: 73.24 - 85.49: 1 85.49 - 97.74: 0 97.74 - 109.99: 1097 109.99 - 122.24: 10123 122.24 - 134.49: 1363 Bond angle restraints: 12584 Sorted by residual: angle pdb=" CE0 WJW F 401 " pdb=" CD9 WJW F 401 " pdb=" OK1 WJW F 401 " ideal model delta sigma weight residual 108.87 73.24 35.63 3.00e+00 1.11e-01 1.41e+02 angle pdb=" CD7 WJW F 401 " pdb=" OD8 WJW F 401 " pdb=" CD9 WJW F 401 " ideal model delta sigma weight residual 109.44 130.52 -21.08 3.00e+00 1.11e-01 4.94e+01 angle pdb=" CE0 WJW F 401 " pdb=" CD9 WJW F 401 " pdb=" OD8 WJW F 401 " ideal model delta sigma weight residual 109.13 124.31 -15.18 3.00e+00 1.11e-01 2.56e+01 angle pdb=" C03 Y75 F 402 " pdb=" N04 Y75 F 402 " pdb=" C05 Y75 F 402 " ideal model delta sigma weight residual 109.52 122.75 -13.23 3.00e+00 1.11e-01 1.94e+01 angle pdb=" N MET G 254 " pdb=" CA MET G 254 " pdb=" C MET G 254 " ideal model delta sigma weight residual 111.28 106.71 4.57 1.09e+00 8.42e-01 1.76e+01 ... (remaining 12579 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.68: 5376 33.68 - 67.36: 151 67.36 - 101.04: 18 101.04 - 134.72: 4 134.72 - 168.40: 5 Dihedral angle restraints: 5554 sinusoidal: 2322 harmonic: 3232 Sorted by residual: dihedral pdb=" C06 Y75 F 402 " pdb=" C32 Y75 F 402 " pdb=" C33 Y75 F 402 " pdb=" C34 Y75 F 402 " ideal model delta sinusoidal sigma weight residual 203.89 35.49 168.40 1 3.00e+01 1.11e-03 2.11e+01 dihedral pdb=" N04 Y75 F 402 " pdb=" C05 Y75 F 402 " pdb=" C06 Y75 F 402 " pdb=" N07 Y75 F 402 " ideal model delta sinusoidal sigma weight residual 254.55 108.98 145.57 1 3.00e+01 1.11e-03 1.95e+01 dihedral pdb=" C4 WJW F 401 " pdb=" C5 WJW F 401 " pdb=" C6 WJW F 401 " pdb=" C7 WJW F 401 " ideal model delta sinusoidal sigma weight residual 162.77 -60.86 -136.37 1 3.00e+01 1.11e-03 1.84e+01 ... (remaining 5551 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.054: 1438 1.054 - 2.108: 0 2.108 - 3.162: 0 3.162 - 4.217: 0 4.217 - 5.271: 1 Chirality restraints: 1439 Sorted by residual: chirality pdb=" CD9 WJW F 401 " pdb=" CE3 WJW F 401 " pdb=" CE0 WJW F 401 " pdb=" OK1 WJW F 401 " both_signs ideal model delta sigma weight residual False -2.58 2.69 -5.27 2.00e-01 2.50e+01 6.94e+02 chirality pdb=" C14 WJW F 401 " pdb=" C15 WJW F 401 " pdb=" CL5 WJW F 401 " pdb=" O13 WJW F 401 " both_signs ideal model delta sigma weight residual False 2.57 2.29 0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C23 WJW F 401 " pdb=" C22 WJW F 401 " pdb=" C39 WJW F 401 " pdb=" O24 WJW F 401 " both_signs ideal model delta sigma weight residual False 2.57 2.32 0.24 2.00e-01 2.50e+01 1.49e+00 ... (remaining 1436 not shown) Planarity restraints: 1559 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C02 Y75 F 402 " -0.082 2.00e-02 2.50e+03 5.62e-01 4.75e+03 pdb=" C03 Y75 F 402 " 0.729 2.00e-02 2.50e+03 pdb=" C43 Y75 F 402 " 0.673 2.00e-02 2.50e+03 pdb=" C44 Y75 F 402 " -0.559 2.00e-02 2.50e+03 pdb=" N42 Y75 F 402 " 0.010 2.00e-02 2.50e+03 pdb=" O01 Y75 F 402 " -0.771 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C03 Y75 F 402 " 0.328 2.00e-02 2.50e+03 2.80e-01 9.77e+02 pdb=" C05 Y75 F 402 " -0.072 2.00e-02 2.50e+03 pdb=" C06 Y75 F 402 " 0.164 2.00e-02 2.50e+03 pdb=" N04 Y75 F 402 " -0.496 2.00e-02 2.50e+03 pdb=" O36 Y75 F 402 " 0.076 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C12 Y75 F 402 " -0.036 2.00e-02 2.50e+03 5.03e-02 6.32e+01 pdb=" C13 Y75 F 402 " -0.022 2.00e-02 2.50e+03 pdb=" C15 Y75 F 402 " 0.004 2.00e-02 2.50e+03 pdb=" C16 Y75 F 402 " 0.008 2.00e-02 2.50e+03 pdb=" C17 Y75 F 402 " -0.006 2.00e-02 2.50e+03 pdb=" C18 Y75 F 402 " 0.070 2.00e-02 2.50e+03 pdb=" C25 Y75 F 402 " -0.039 2.00e-02 2.50e+03 pdb=" C26 Y75 F 402 " -0.070 2.00e-02 2.50e+03 pdb=" S11 Y75 F 402 " 0.108 2.00e-02 2.50e+03 pdb="CL14 Y75 F 402 " -0.016 2.00e-02 2.50e+03 ... (remaining 1556 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 70 2.56 - 3.15: 7201 3.15 - 3.73: 14655 3.73 - 4.32: 20515 4.32 - 4.90: 34671 Nonbonded interactions: 77112 Sorted by model distance: nonbonded pdb=" OE1 WJW F 401 " pdb=" OK1 WJW F 401 " model vdw 1.977 2.432 nonbonded pdb=" OG1 THR G 23 " pdb=" OG SER G 70 " model vdw 2.196 2.440 nonbonded pdb=" OH TYR G 317 " pdb=" O28 WJW F 401 " model vdw 2.238 2.440 nonbonded pdb=" OD1 ASP B 202 " pdb=" N ASN B 204 " model vdw 2.239 2.520 nonbonded pdb=" OC4 WJW F 401 " pdb=" OK0 WJW F 401 " model vdw 2.246 2.440 ... (remaining 77107 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 10 through 247) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.940 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 28.930 Find NCS groups from input model: 0.380 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7997 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 : 0.009 0.224 9308 Z= 0.527 Angle : 0.913 35.626 12584 Z= 0.395 Chirality : 0.146 5.271 1439 Planarity : 0.016 0.562 1559 Dihedral : 16.701 168.399 3476 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.25), residues: 1100 helix: 1.44 (0.21), residues: 593 sheet: 0.99 (0.44), residues: 134 loop : -0.67 (0.32), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP F 119 HIS 0.002 0.000 HIS A 81 PHE 0.010 0.001 PHE F 109 TYR 0.009 0.001 TYR F 333 ARG 0.008 0.001 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.975 Fit side-chains REVERT: A 204 ASN cc_start: 0.8234 (t0) cc_final: 0.7671 (t0) REVERT: A 207 GLU cc_start: 0.7055 (mm-30) cc_final: 0.6455 (mm-30) REVERT: B 96 SER cc_start: 0.9371 (p) cc_final: 0.8876 (t) REVERT: B 163 ASP cc_start: 0.7734 (t0) cc_final: 0.7346 (t70) REVERT: B 240 LYS cc_start: 0.8370 (ttmm) cc_final: 0.8153 (ttmm) REVERT: F 166 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7191 (mtp85) REVERT: G 301 MET cc_start: 0.8429 (tpp) cc_final: 0.8226 (mmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2524 time to fit residues: 35.9502 Evaluate side-chains 93 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.9980 chunk 82 optimal weight: 0.8980 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 85 optimal weight: 3.9990 chunk 33 optimal weight: 5.9990 chunk 51 optimal weight: 0.7980 chunk 63 optimal weight: 0.0870 chunk 98 optimal weight: 2.9990 overall best weight: 1.1560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN G 173 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.0705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 9308 Z= 0.263 Angle : 0.682 25.877 12584 Z= 0.294 Chirality : 0.074 2.239 1439 Planarity : 0.004 0.047 1559 Dihedral : 14.402 169.151 1354 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 0.74 % Allowed : 5.78 % Favored : 93.48 % 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 (0.25), residues: 1100 helix: 1.34 (0.21), residues: 596 sheet: 0.77 (0.44), residues: 138 loop : -0.57 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 119 HIS 0.002 0.001 HIS G 10 PHE 0.011 0.001 PHE B 32 TYR 0.009 0.001 TYR F 6 ARG 0.006 0.000 ARG F 212 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 104 time to evaluate : 1.160 Fit side-chains REVERT: B 163 ASP cc_start: 0.7726 (t0) cc_final: 0.7302 (t70) REVERT: B 240 LYS cc_start: 0.8420 (ttmm) cc_final: 0.8215 (ttmm) REVERT: G 258 ARG cc_start: 0.8110 (ttp80) cc_final: 0.6167 (mtt180) outliers start: 7 outliers final: 5 residues processed: 108 average time/residue: 0.2769 time to fit residues: 41.4873 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 101 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 88 optimal weight: 1.9990 chunk 98 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 0.7980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.0843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9308 Z= 0.209 Angle : 0.637 22.914 12584 Z= 0.276 Chirality : 0.073 2.250 1439 Planarity : 0.003 0.047 1559 Dihedral : 13.954 167.518 1354 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.16 % Allowed : 8.20 % Favored : 90.64 % 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: 0.94 (0.25), residues: 1100 helix: 1.35 (0.21), residues: 595 sheet: 0.90 (0.45), residues: 136 loop : -0.61 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 119 HIS 0.002 0.001 HIS A 81 PHE 0.009 0.001 PHE B 32 TYR 0.008 0.001 TYR F 6 ARG 0.006 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 103 time to evaluate : 1.055 Fit side-chains REVERT: B 163 ASP cc_start: 0.7672 (t0) cc_final: 0.7232 (t70) REVERT: B 240 LYS cc_start: 0.8427 (ttmm) cc_final: 0.8213 (ttmm) REVERT: G 258 ARG cc_start: 0.8119 (ttp80) cc_final: 0.6197 (mtt180) outliers start: 11 outliers final: 7 residues processed: 111 average time/residue: 0.2609 time to fit residues: 38.8299 Evaluate side-chains 106 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 99 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 47 optimal weight: 0.5980 chunk 66 optimal weight: 4.9990 chunk 99 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 7.9990 chunk 28 optimal weight: 0.0870 chunk 87 optimal weight: 1.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8093 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9308 Z= 0.224 Angle : 0.634 24.056 12584 Z= 0.276 Chirality : 0.072 2.224 1439 Planarity : 0.003 0.048 1559 Dihedral : 13.681 164.255 1354 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.64 % Favored : 98.36 % Rotamer: Outliers : 1.37 % Allowed : 9.78 % Favored : 88.85 % 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 (0.25), residues: 1100 helix: 1.34 (0.21), residues: 599 sheet: 0.91 (0.46), residues: 128 loop : -0.61 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 271 HIS 0.002 0.001 HIS A 81 PHE 0.009 0.001 PHE B 32 TYR 0.009 0.001 TYR F 6 ARG 0.007 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 1.091 Fit side-chains REVERT: B 163 ASP cc_start: 0.7670 (t0) cc_final: 0.7223 (t70) REVERT: G 258 ARG cc_start: 0.8121 (ttp80) cc_final: 0.6208 (mtt180) outliers start: 13 outliers final: 12 residues processed: 110 average time/residue: 0.2542 time to fit residues: 38.2308 Evaluate side-chains 110 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 89 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 94 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.067 9308 Z= 0.521 Angle : 0.757 23.724 12584 Z= 0.342 Chirality : 0.076 2.245 1439 Planarity : 0.004 0.050 1559 Dihedral : 13.775 164.588 1354 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.21 % Allowed : 11.78 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.25), residues: 1100 helix: 0.61 (0.20), residues: 601 sheet: 0.42 (0.45), residues: 130 loop : -0.61 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 271 HIS 0.004 0.001 HIS A 214 PHE 0.016 0.002 PHE F 69 TYR 0.015 0.001 TYR F 6 ARG 0.005 0.001 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 101 time to evaluate : 1.016 Fit side-chains REVERT: A 67 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7535 (pt0) REVERT: B 163 ASP cc_start: 0.7720 (t0) cc_final: 0.7288 (t70) REVERT: G 258 ARG cc_start: 0.8151 (ttp80) cc_final: 0.6142 (mtt180) outliers start: 21 outliers final: 16 residues processed: 117 average time/residue: 0.2555 time to fit residues: 40.0334 Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 8.9990 chunk 20 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.5980 chunk 48 optimal weight: 0.5980 chunk 8 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.1504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9308 Z= 0.211 Angle : 0.640 23.948 12584 Z= 0.280 Chirality : 0.072 2.214 1439 Planarity : 0.004 0.050 1559 Dihedral : 13.503 165.445 1354 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 1.79 % Allowed : 13.25 % Favored : 84.96 % 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: 0.53 (0.25), residues: 1100 helix: 1.00 (0.21), residues: 595 sheet: 0.52 (0.45), residues: 128 loop : -0.64 (0.32), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 119 HIS 0.002 0.000 HIS A 69 PHE 0.010 0.001 PHE B 32 TYR 0.009 0.001 TYR F 6 ARG 0.006 0.000 ARG A 114 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 101 time to evaluate : 1.103 Fit side-chains REVERT: A 67 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.7578 (pt0) REVERT: A 204 ASN cc_start: 0.8224 (t0) cc_final: 0.7756 (t0) REVERT: B 163 ASP cc_start: 0.7674 (t0) cc_final: 0.7255 (t70) REVERT: B 204 ASN cc_start: 0.8513 (t0) cc_final: 0.7798 (t0) REVERT: G 258 ARG cc_start: 0.8108 (ttp80) cc_final: 0.6093 (mtt180) outliers start: 17 outliers final: 13 residues processed: 112 average time/residue: 0.2623 time to fit residues: 39.6574 Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 1.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 65 optimal weight: 9.9990 chunk 64 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 41 optimal weight: 0.0980 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 9308 Z= 0.340 Angle : 0.676 23.865 12584 Z= 0.300 Chirality : 0.073 2.232 1439 Planarity : 0.004 0.050 1559 Dihedral : 13.482 165.800 1354 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.10 % Allowed : 13.46 % Favored : 84.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.25), residues: 1100 helix: 0.91 (0.21), residues: 591 sheet: 0.46 (0.45), residues: 128 loop : -0.65 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 271 HIS 0.002 0.001 HIS A 214 PHE 0.012 0.001 PHE F 69 TYR 0.012 0.001 TYR F 6 ARG 0.007 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 98 time to evaluate : 1.015 Fit side-chains REVERT: A 67 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7563 (pt0) REVERT: B 163 ASP cc_start: 0.7712 (t0) cc_final: 0.7290 (t70) REVERT: B 204 ASN cc_start: 0.8566 (t0) cc_final: 0.7856 (t0) REVERT: G 258 ARG cc_start: 0.8135 (ttp80) cc_final: 0.6109 (mtt180) outliers start: 20 outliers final: 15 residues processed: 113 average time/residue: 0.2322 time to fit residues: 35.9502 Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 97 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 20 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 chunk 100 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 9308 Z= 0.293 Angle : 0.663 23.916 12584 Z= 0.292 Chirality : 0.073 2.225 1439 Planarity : 0.004 0.051 1559 Dihedral : 13.397 165.625 1354 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.89 % Allowed : 14.20 % Favored : 83.91 % 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: 0.46 (0.25), residues: 1100 helix: 0.95 (0.21), residues: 591 sheet: 0.40 (0.45), residues: 128 loop : -0.63 (0.31), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 119 HIS 0.002 0.001 HIS A 214 PHE 0.010 0.001 PHE F 69 TYR 0.011 0.001 TYR F 6 ARG 0.008 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 98 time to evaluate : 0.967 Fit side-chains REVERT: A 67 GLU cc_start: 0.7855 (OUTLIER) cc_final: 0.7543 (pt0) REVERT: B 163 ASP cc_start: 0.7668 (t0) cc_final: 0.7264 (t70) REVERT: B 204 ASN cc_start: 0.8504 (t0) cc_final: 0.7852 (t0) REVERT: G 258 ARG cc_start: 0.8123 (ttp80) cc_final: 0.6101 (mtt180) outliers start: 18 outliers final: 15 residues processed: 111 average time/residue: 0.2461 time to fit residues: 37.2073 Evaluate side-chains 110 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 94 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 76 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 chunk 103 optimal weight: 0.4980 chunk 63 optimal weight: 3.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 9308 Z= 0.308 Angle : 0.669 23.896 12584 Z= 0.296 Chirality : 0.073 2.228 1439 Planarity : 0.004 0.051 1559 Dihedral : 13.348 165.797 1354 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.21 % Allowed : 14.41 % Favored : 83.39 % 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: 0.42 (0.25), residues: 1100 helix: 0.94 (0.21), residues: 585 sheet: 0.36 (0.44), residues: 128 loop : -0.65 (0.31), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 272 HIS 0.002 0.001 HIS A 214 PHE 0.011 0.001 PHE F 69 TYR 0.011 0.001 TYR F 6 ARG 0.008 0.000 ARG F 295 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 97 time to evaluate : 0.962 Fit side-chains REVERT: A 67 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7542 (pt0) REVERT: A 204 ASN cc_start: 0.8289 (t0) cc_final: 0.7961 (t0) REVERT: A 207 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6641 (mm-30) REVERT: B 163 ASP cc_start: 0.7686 (t0) cc_final: 0.7274 (t70) REVERT: B 204 ASN cc_start: 0.8497 (t0) cc_final: 0.7892 (t0) REVERT: G 258 ARG cc_start: 0.8140 (ttp80) cc_final: 0.6096 (mtt180) outliers start: 21 outliers final: 17 residues processed: 113 average time/residue: 0.2407 time to fit residues: 37.1665 Evaluate side-chains 112 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 128 GLU Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.5980 chunk 71 optimal weight: 0.9980 chunk 108 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 chunk 53 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9308 Z= 0.206 Angle : 0.638 24.042 12584 Z= 0.280 Chirality : 0.072 2.215 1439 Planarity : 0.004 0.051 1559 Dihedral : 13.261 166.312 1354 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.89 % Allowed : 14.72 % Favored : 83.39 % 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: 0.63 (0.25), residues: 1100 helix: 1.15 (0.21), residues: 589 sheet: 0.40 (0.44), residues: 128 loop : -0.62 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 271 HIS 0.002 0.001 HIS B 69 PHE 0.011 0.001 PHE B 32 TYR 0.008 0.001 TYR F 6 ARG 0.008 0.000 ARG F 295 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2200 Ramachandran restraints generated. 1100 Oldfield, 0 Emsley, 1100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 96 time to evaluate : 1.077 Fit side-chains REVERT: A 67 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7546 (pt0) REVERT: A 207 GLU cc_start: 0.7263 (mm-30) cc_final: 0.6748 (mm-30) REVERT: B 163 ASP cc_start: 0.7674 (t0) cc_final: 0.7265 (t70) REVERT: B 204 ASN cc_start: 0.8391 (t0) cc_final: 0.7874 (t0) REVERT: G 258 ARG cc_start: 0.8128 (ttp80) cc_final: 0.6092 (mtt180) outliers start: 18 outliers final: 16 residues processed: 110 average time/residue: 0.2464 time to fit residues: 37.1352 Evaluate side-chains 113 residues out of total 953 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 96 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 102 THR Chi-restraints excluded: chain A residue 138 ILE Chi-restraints excluded: chain A residue 140 ASP Chi-restraints excluded: chain A residue 191 LEU Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain B residue 128 GLU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 233 LEU Chi-restraints excluded: chain F residue 330 VAL Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 195 VAL Chi-restraints excluded: chain G residue 275 VAL Chi-restraints excluded: chain G residue 290 SER Chi-restraints excluded: chain G residue 328 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 0.2980 chunk 86 optimal weight: 0.1980 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.129725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.095830 restraints weight = 10111.623| |-----------------------------------------------------------------------------| r_work (start): 0.2952 rms_B_bonded: 1.54 r_work: 0.2815 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2687 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9308 Z= 0.236 Angle : 0.649 24.068 12584 Z= 0.285 Chirality : 0.072 2.220 1439 Planarity : 0.004 0.051 1559 Dihedral : 13.235 166.618 1354 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 2.10 % Allowed : 14.62 % Favored : 83.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1100 helix: 1.10 (0.21), residues: 597 sheet: 0.41 (0.44), residues: 128 loop : -0.61 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 119 HIS 0.002 0.001 HIS A 81 PHE 0.009 0.001 PHE F 69 TYR 0.009 0.001 TYR F 6 ARG 0.008 0.000 ARG F 295 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2019.33 seconds wall clock time: 37 minutes 44.42 seconds (2264.42 seconds total)