Starting phenix.real_space_refine on Mon Mar 11 19:17:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8frn_29402/03_2024/8frn_29402_neut_updated.pdb" } resolution = 3.3 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= 0.028 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 39 5.16 5 C 5624 2.51 5 N 1447 2.21 5 O 1531 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 130": "NH1" <-> "NH2" Residue "G GLU 145": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8643 Number of models: 1 Model: "" Number of chains: 6 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: 2282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2282 Classifications: {'peptide': 289} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 276} Chain breaks: 2 Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "G" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 2386 Classifications: {'peptide': 297} Link IDs: {'PTRANS': 11, 'TRANS': 285} Chain breaks: 6 Chain: "F" Number of atoms: 195 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 195 Unusual residues: {'JSG': 1, 'VB6': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 25 Planarities with less than four sites: {'JSG:plan-7': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'LMT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.07, per 1000 atoms: 0.59 Number of scatterers: 8643 At special positions: 0 Unit cell: (71.38, 132.8, 94.62, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 39 16.00 P 2 15.00 O 1531 8.00 N 1447 7.00 C 5624 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: 3.45 Conformation dependent library (CDL) restraints added in 1.6 seconds 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 45 helices and 8 sheets defined 55.3% alpha, 9.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.58 Creating SS restraints... Processing helix chain 'A' and resid 50 through 58 Processing helix chain 'A' and resid 80 through 86 removed outlier: 3.619A pdb=" N LYS A 86 " --> pdb=" O GLU A 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.793A pdb=" N ILE A 110 " --> pdb=" O ASN A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 132 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 162 removed outlier: 3.724A pdb=" N ALA A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 178 through 193 removed outlier: 4.287A pdb=" N GLY A 182 " --> pdb=" O PRO A 178 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N ASP A 183 " --> pdb=" O ILE A 179 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 removed outlier: 3.918A 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 removed outlier: 3.531A pdb=" N VAL A 241 " --> pdb=" O GLN A 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 58 Processing helix chain 'B' and resid 80 through 86 removed outlier: 3.783A pdb=" N LYS B 86 " --> pdb=" O GLU B 82 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.566A pdb=" N ILE B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 132 removed outlier: 3.622A pdb=" N GLN B 123 " --> pdb=" O LYS B 119 " (cutoff:3.500A) removed outlier: 3.668A 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 143 through 145 No H-bonds generated for 'chain 'B' and resid 143 through 145' Processing helix chain 'B' and resid 148 through 162 removed outlier: 3.950A pdb=" N ALA B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 Processing helix chain 'B' and resid 205 through 211 removed outlier: 4.183A pdb=" N ALA B 210 " --> pdb=" O ARG B 206 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ILE B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) 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 40 removed outlier: 3.669A pdb=" N ARG F 30 " --> pdb=" O MET F 26 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLN F 40 " --> pdb=" O GLY F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 48 through 54 removed outlier: 3.543A pdb=" N ILE F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 81 removed outlier: 4.019A 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 86 through 89 No H-bonds generated for 'chain 'F' and resid 86 through 89' Processing helix chain 'F' and resid 95 through 118 removed outlier: 3.806A pdb=" N LEU F 102 " --> pdb=" O LEU F 98 " (cutoff:3.500A) removed outlier: 3.836A 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 253 through 257 Processing helix chain 'F' and resid 263 through 273 removed outlier: 3.582A pdb=" N GLY F 270 " --> pdb=" O ALA F 266 " (cutoff:3.500A) Processing helix chain 'F' and resid 276 through 288 removed outlier: 3.545A pdb=" N VAL F 280 " --> pdb=" O PHE F 277 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N MET F 284 " --> pdb=" O ILE F 281 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N MET F 285 " --> pdb=" O ALA F 282 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA F 286 " --> pdb=" O LEU F 283 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N VAL F 287 " --> pdb=" O MET F 284 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ALA F 288 " --> pdb=" O MET F 285 " (cutoff:3.500A) Processing helix chain 'F' and resid 300 through 324 Proline residue: F 304 - end of helix removed outlier: 3.516A pdb=" N PHE F 307 " --> pdb=" O ILE F 303 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE F 308 " --> pdb=" O PRO F 304 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU F 312 " --> pdb=" O ILE F 308 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG F 322 " --> pdb=" O ALA F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 349 Proline residue: F 334 - end of helix removed outlier: 3.734A pdb=" N VAL F 339 " --> pdb=" O ALA F 336 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE F 342 " --> pdb=" O VAL F 339 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA F 343 " --> pdb=" O TYR F 340 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA F 344 " --> pdb=" O GLY F 341 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU F 346 " --> pdb=" O ALA F 343 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER F 348 " --> pdb=" O ALA F 345 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 41 removed outlier: 4.050A pdb=" N SER G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ASN G 41 " --> pdb=" O GLY G 37 " (cutoff:3.500A) Processing helix chain 'G' and resid 48 through 57 removed outlier: 3.821A pdb=" N TYR G 54 " --> pdb=" O GLN G 50 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL G 55 " --> pdb=" O ALA G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 84 Proline residue: G 68 - end of helix removed outlier: 3.625A pdb=" N LEU G 82 " --> pdb=" O GLY G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 87 through 94 removed outlier: 3.714A pdb=" N VAL G 94 " --> pdb=" O VAL G 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 98 through 122 removed outlier: 3.557A pdb=" N SER G 108 " --> pdb=" O TRP G 104 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N VAL G 111 " --> pdb=" O ARG G 107 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU G 112 " --> pdb=" O SER G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 124 through 135 removed outlier: 3.804A pdb=" N GLU G 129 " --> pdb=" O PRO G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 232 through 237 removed outlier: 4.398A pdb=" N HIS G 236 " --> pdb=" O LYS G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 247 through 260 removed outlier: 3.710A pdb=" N TYR G 260 " --> pdb=" O TYR G 256 " (cutoff:3.500A) 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: 3.716A 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: 6.517A pdb=" N ILE A 217 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU A 226 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA A 215 " --> pdb=" O GLU A 226 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N HIS A 214 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N VAL A 198 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N LEU A 42 " --> pdb=" O VAL A 198 " (cutoff:3.500A) removed outlier: 6.301A 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: 7.789A pdb=" N LYS A 19 " --> pdb=" O LYS A 28 " (cutoff:3.500A) removed outlier: 5.676A 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: 6.853A pdb=" N ILE B 217 " --> pdb=" O ILE B 224 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU B 226 " --> pdb=" O ALA B 215 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N ALA B 215 " --> pdb=" O GLU B 226 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N HIS B 214 " --> pdb=" O ILE B 39 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N VAL B 198 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N LEU B 42 " --> pdb=" O VAL B 198 " (cutoff:3.500A) removed outlier: 6.164A 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: 7.779A pdb=" N LYS B 19 " --> pdb=" O LYS B 28 " (cutoff:3.500A) removed outlier: 5.500A 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: 4.269A pdb=" N GLU F 148 " --> pdb=" O ALA F 159 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA F 159 " --> pdb=" O GLU F 148 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'G' and resid 157 through 160 415 hydrogen bonds defined for protein. 1167 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: 2.25 Time building geometry restraints manager: 3.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1355 1.32 - 1.44: 2296 1.44 - 1.56: 5081 1.56 - 1.68: 2 1.68 - 1.81: 72 Bond restraints: 8806 Sorted by residual: bond pdb=" C7 JSG F 401 " pdb=" N2 JSG F 401 " ideal model delta sigma weight residual 1.621 1.315 0.306 2.00e-02 2.50e+03 2.34e+02 bond pdb=" C02 VB6 F 402 " pdb=" N34 VB6 F 402 " ideal model delta sigma weight residual 1.532 1.331 0.201 2.00e-02 2.50e+03 1.01e+02 bond pdb=" C08 VB6 F 402 " pdb=" N07 VB6 F 402 " ideal model delta sigma weight residual 1.523 1.338 0.185 2.00e-02 2.50e+03 8.59e+01 bond pdb=" CDO JSG F 401 " pdb=" NAO JSG F 401 " ideal model delta sigma weight residual 1.505 1.321 0.184 2.00e-02 2.50e+03 8.48e+01 bond pdb=" C05 VB6 F 402 " pdb=" N04 VB6 F 402 " ideal model delta sigma weight residual 1.513 1.349 0.164 2.00e-02 2.50e+03 6.72e+01 ... (remaining 8801 not shown) Histogram of bond angle deviations from ideal: 97.33 - 104.74: 128 104.74 - 112.16: 4480 112.16 - 119.58: 3100 119.58 - 126.99: 4095 126.99 - 134.41: 84 Bond angle restraints: 11887 Sorted by residual: angle pdb=" C09 VB6 F 402 " pdb=" N10 VB6 F 402 " pdb=" C11 VB6 F 402 " ideal model delta sigma weight residual 141.52 117.11 24.41 3.00e+00 1.11e-01 6.62e+01 angle pdb=" N ILE F 323 " pdb=" CA ILE F 323 " pdb=" C ILE F 323 " ideal model delta sigma weight residual 111.58 106.56 5.02 1.06e+00 8.90e-01 2.24e+01 angle pdb=" C03 VB6 F 402 " pdb=" N04 VB6 F 402 " pdb=" C05 VB6 F 402 " ideal model delta sigma weight residual 109.37 123.58 -14.21 3.00e+00 1.11e-01 2.24e+01 angle pdb=" C02 VB6 F 402 " pdb=" N34 VB6 F 402 " pdb=" C35 VB6 F 402 " ideal model delta sigma weight residual 109.43 122.27 -12.84 3.00e+00 1.11e-01 1.83e+01 angle pdb=" C06 VB6 F 402 " pdb=" N07 VB6 F 402 " pdb=" C08 VB6 F 402 " ideal model delta sigma weight residual 109.80 122.55 -12.75 3.00e+00 1.11e-01 1.81e+01 ... (remaining 11882 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.11: 5036 28.11 - 56.22: 243 56.22 - 84.33: 24 84.33 - 112.44: 5 112.44 - 140.55: 3 Dihedral angle restraints: 5311 sinusoidal: 2249 harmonic: 3062 Sorted by residual: dihedral pdb=" N07 VB6 F 402 " pdb=" C08 VB6 F 402 " pdb=" C09 VB6 F 402 " pdb=" N10 VB6 F 402 " ideal model delta sinusoidal sigma weight residual 215.27 74.72 140.55 1 3.00e+01 1.11e-03 1.89e+01 dihedral pdb=" C12 VB6 F 402 " pdb=" C13 VB6 F 402 " pdb=" C14 VB6 F 402 " pdb=" N15 VB6 F 402 " ideal model delta sinusoidal sigma weight residual 164.10 -64.92 -130.98 1 3.00e+01 1.11e-03 1.77e+01 dihedral pdb=" CGQ JSG F 401 " pdb=" CGN JSG F 401 " pdb=" CGP JSG F 401 " pdb=" OFZ JSG F 401 " ideal model delta sinusoidal sigma weight residual 144.32 29.46 114.86 1 3.00e+01 1.11e-03 1.52e+01 ... (remaining 5308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.088: 1231 0.088 - 0.175: 120 0.175 - 0.263: 13 0.263 - 0.350: 2 0.350 - 0.438: 1 Chirality restraints: 1367 Sorted by residual: chirality pdb=" C03 VB6 F 402 " pdb=" C02 VB6 F 402 " pdb=" C24 VB6 F 402 " pdb=" N04 VB6 F 402 " both_signs ideal model delta sigma weight residual False 2.64 2.21 0.44 2.00e-01 2.50e+01 4.79e+00 chirality pdb=" CA GLN A 121 " pdb=" N GLN A 121 " pdb=" C GLN A 121 " pdb=" CB GLN A 121 " both_signs ideal model delta sigma weight residual False 2.51 2.79 -0.28 2.00e-01 2.50e+01 1.96e+00 chirality pdb=" CAN JSG F 401 " pdb=" CAL JSG F 401 " pdb=" CAP JSG F 401 " pdb=" NAO JSG F 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.80 0.27 2.00e-01 2.50e+01 1.79e+00 ... (remaining 1364 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C03 VB6 F 402 " 0.317 2.00e-02 2.50e+03 2.88e-01 1.25e+03 pdb=" C05 VB6 F 402 " 0.039 2.00e-02 2.50e+03 pdb=" C06 VB6 F 402 " -0.363 2.00e-02 2.50e+03 pdb=" C23 VB6 F 402 " -0.363 2.00e-02 2.50e+03 pdb=" N04 VB6 F 402 " 0.005 2.00e-02 2.50e+03 pdb=" O22 VB6 F 402 " 0.365 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C35 VB6 F 402 " -0.076 2.00e-02 2.50e+03 4.30e-02 4.16e+01 pdb=" C36 VB6 F 402 " -0.011 2.00e-02 2.50e+03 pdb=" C37 VB6 F 402 " -0.001 2.00e-02 2.50e+03 pdb=" C38 VB6 F 402 " 0.070 2.00e-02 2.50e+03 pdb=" C47 VB6 F 402 " -0.011 2.00e-02 2.50e+03 pdb=" C48 VB6 F 402 " -0.015 2.00e-02 2.50e+03 pdb=" C49 VB6 F 402 " -0.018 2.00e-02 2.50e+03 pdb=" C50 VB6 F 402 " -0.010 2.00e-02 2.50e+03 pdb=" S51 VB6 F 402 " 0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C06 VB6 F 402 " -0.024 2.00e-02 2.50e+03 2.05e-02 5.23e+00 pdb=" C08 VB6 F 402 " -0.003 2.00e-02 2.50e+03 pdb=" C09 VB6 F 402 " -0.016 2.00e-02 2.50e+03 pdb=" N07 VB6 F 402 " 0.035 2.00e-02 2.50e+03 pdb=" O16 VB6 F 402 " 0.008 2.00e-02 2.50e+03 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 1.42 - 2.11: 2 2.11 - 2.81: 2393 2.81 - 3.51: 11650 3.51 - 4.20: 20926 4.20 - 4.90: 37611 Nonbonded interactions: 72582 Sorted by model distance: nonbonded pdb=" CBE JSG F 401 " pdb=" OBU JSG F 401 " model vdw 1.416 3.470 nonbonded pdb=" CBC JSG F 401 " pdb=" OBS JSG F 401 " model vdw 1.421 3.470 nonbonded pdb=" O ASP B 71 " pdb=" OD1 ASN B 72 " model vdw 2.165 3.040 nonbonded pdb=" O ASN G 41 " pdb=" OD1 ASN G 41 " model vdw 2.167 3.040 nonbonded pdb=" OD2 ASP G 161 " pdb=" NH1 ARG G 171 " model vdw 2.257 2.520 ... (remaining 72577 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: 0.760 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: 3.960 Check model and map are aligned: 0.180 Set scattering table: 0.070 Process input model: 26.960 Find NCS groups from input model: 0.380 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 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 : 0.010 0.306 8806 Z= 0.614 Angle : 0.860 24.407 11887 Z= 0.463 Chirality : 0.053 0.438 1367 Planarity : 0.008 0.288 1463 Dihedral : 15.807 140.546 3339 Min Nonbonded Distance : 1.416 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.11 % Allowed : 1.44 % Favored : 98.45 % 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: -1.45 (0.25), residues: 1039 helix: -0.95 (0.20), residues: 592 sheet: 1.50 (0.61), residues: 85 loop : -1.36 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 49 HIS 0.003 0.001 HIS B 214 PHE 0.007 0.001 PHE A 133 TYR 0.007 0.001 TYR F 333 ARG 0.002 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 312 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: A 11 THR cc_start: 0.9154 (m) cc_final: 0.8914 (t) REVERT: A 15 LYS cc_start: 0.6827 (mttt) cc_final: 0.6096 (mmtp) REVERT: A 19 LYS cc_start: 0.8255 (tptt) cc_final: 0.8054 (tptp) REVERT: A 35 GLN cc_start: 0.7898 (mt0) cc_final: 0.7628 (mp10) REVERT: A 102 THR cc_start: 0.7668 (m) cc_final: 0.7279 (p) REVERT: A 140 ASP cc_start: 0.8272 (m-30) cc_final: 0.7867 (m-30) REVERT: A 167 MET cc_start: 0.8489 (tpp) cc_final: 0.8231 (mmm) REVERT: A 179 ILE cc_start: 0.8658 (tp) cc_final: 0.8351 (tp) REVERT: A 239 ARG cc_start: 0.7915 (mtm-85) cc_final: 0.7394 (ttm-80) REVERT: B 10 GLN cc_start: 0.6818 (mt0) cc_final: 0.6136 (mt0) REVERT: B 112 GLU cc_start: 0.8732 (mt-10) cc_final: 0.8530 (mt-10) REVERT: B 125 ARG cc_start: 0.8447 (tpt170) cc_final: 0.8002 (tpt170) REVERT: B 127 GLN cc_start: 0.8889 (tp-100) cc_final: 0.8683 (tp-100) REVERT: B 155 GLU cc_start: 0.8140 (mt-10) cc_final: 0.7843 (mt-10) REVERT: G 12 THR cc_start: 0.8365 (m) cc_final: 0.7970 (p) REVERT: G 126 TYR cc_start: 0.8311 (t80) cc_final: 0.7808 (t80) REVERT: G 162 TYR cc_start: 0.7515 (t80) cc_final: 0.7232 (t80) outliers start: 1 outliers final: 0 residues processed: 313 average time/residue: 0.2491 time to fit residues: 101.5015 Evaluate side-chains 188 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 43 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 41 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 0.3980 chunk 60 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 121 GLN A 131 ASN B 204 ASN B 214 HIS G 41 ASN G 50 GLN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8806 Z= 0.291 Angle : 0.642 7.538 11887 Z= 0.317 Chirality : 0.044 0.178 1367 Planarity : 0.005 0.049 1463 Dihedral : 11.627 114.186 1336 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 11.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 2.22 % Allowed : 12.99 % Favored : 84.79 % 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: -0.14 (0.25), residues: 1039 helix: 0.33 (0.21), residues: 582 sheet: 1.26 (0.54), residues: 95 loop : -1.02 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP F 123 HIS 0.004 0.001 HIS A 69 PHE 0.014 0.001 PHE F 274 TYR 0.020 0.001 TYR G 64 ARG 0.012 0.001 ARG A 122 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 199 time to evaluate : 0.953 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6893 (mttt) cc_final: 0.6346 (mmtp) REVERT: A 167 MET cc_start: 0.8544 (tpp) cc_final: 0.8249 (tpp) REVERT: A 239 ARG cc_start: 0.8163 (mtm-85) cc_final: 0.7345 (mtp85) REVERT: B 58 VAL cc_start: 0.8406 (t) cc_final: 0.8043 (m) REVERT: B 67 GLU cc_start: 0.7676 (mt-10) cc_final: 0.7448 (mt-10) REVERT: B 124 GLN cc_start: 0.8550 (tm-30) cc_final: 0.8311 (tm-30) REVERT: B 125 ARG cc_start: 0.8515 (tpt170) cc_final: 0.7870 (tpt170) REVERT: B 204 ASN cc_start: 0.8556 (t0) cc_final: 0.8012 (t0) REVERT: F 80 TYR cc_start: 0.8638 (m-80) cc_final: 0.8408 (m-80) REVERT: F 156 THR cc_start: 0.8272 (p) cc_final: 0.8039 (p) REVERT: F 328 LEU cc_start: 0.8722 (tp) cc_final: 0.8354 (tp) outliers start: 20 outliers final: 14 residues processed: 209 average time/residue: 0.2221 time to fit residues: 64.4095 Evaluate side-chains 179 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 165 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 SER Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 120 MET Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 51 optimal weight: 2.9990 chunk 29 optimal weight: 0.0000 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 93 optimal weight: 6.9990 chunk 101 optimal weight: 0.6980 chunk 83 optimal weight: 0.5980 chunk 92 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 overall best weight: 0.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN A 131 ASN A 204 ASN B 10 GLN B 81 HIS ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 40 GLN F 100 GLN G 41 ASN ** G 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8806 Z= 0.173 Angle : 0.533 6.860 11887 Z= 0.265 Chirality : 0.042 0.205 1367 Planarity : 0.004 0.052 1463 Dihedral : 11.148 118.219 1336 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 2.11 % Allowed : 17.54 % Favored : 80.36 % 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: 0.56 (0.26), residues: 1039 helix: 1.08 (0.21), residues: 576 sheet: 0.84 (0.48), residues: 114 loop : -0.92 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 123 HIS 0.003 0.001 HIS A 81 PHE 0.022 0.001 PHE F 274 TYR 0.018 0.001 TYR G 260 ARG 0.004 0.000 ARG F 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 185 time to evaluate : 0.968 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6879 (mttt) cc_final: 0.6311 (mmtp) REVERT: A 167 MET cc_start: 0.8534 (tpp) cc_final: 0.8271 (tpp) REVERT: A 239 ARG cc_start: 0.8124 (mtm-85) cc_final: 0.7378 (mtp85) REVERT: B 58 VAL cc_start: 0.8376 (t) cc_final: 0.7988 (m) REVERT: B 125 ARG cc_start: 0.8574 (tpt170) cc_final: 0.8199 (tpt170) REVERT: B 163 ASP cc_start: 0.7018 (m-30) cc_final: 0.6694 (m-30) REVERT: B 204 ASN cc_start: 0.8581 (t0) cc_final: 0.8096 (t0) REVERT: F 156 THR cc_start: 0.8301 (p) cc_final: 0.8053 (p) outliers start: 19 outliers final: 10 residues processed: 190 average time/residue: 0.2053 time to fit residues: 53.6706 Evaluate side-chains 166 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 156 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 176 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 92 optimal weight: 8.9990 chunk 70 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 62 optimal weight: 9.9990 chunk 94 optimal weight: 0.4980 chunk 99 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 89 optimal weight: 20.0000 chunk 26 optimal weight: 7.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 100 GLN G 41 ASN G 262 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8806 Z= 0.291 Angle : 0.577 6.931 11887 Z= 0.285 Chirality : 0.044 0.138 1367 Planarity : 0.004 0.051 1463 Dihedral : 10.854 114.403 1336 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 10.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.89 % Allowed : 20.31 % Favored : 76.80 % 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: 0.75 (0.26), residues: 1039 helix: 1.25 (0.22), residues: 587 sheet: 0.71 (0.47), residues: 115 loop : -0.85 (0.33), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 271 HIS 0.004 0.001 HIS A 81 PHE 0.019 0.002 PHE G 253 TYR 0.013 0.001 TYR F 299 ARG 0.004 0.000 ARG A 152 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 171 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7067 (mttt) cc_final: 0.6473 (mmtp) REVERT: A 167 MET cc_start: 0.8581 (tpp) cc_final: 0.8311 (tpp) REVERT: A 216 TYR cc_start: 0.8524 (m-80) cc_final: 0.8150 (m-80) REVERT: A 239 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7438 (mtp85) REVERT: B 163 ASP cc_start: 0.7149 (m-30) cc_final: 0.6838 (m-30) REVERT: F 156 THR cc_start: 0.8340 (p) cc_final: 0.8084 (p) REVERT: G 62 TYR cc_start: 0.8690 (m-80) cc_final: 0.8472 (m-80) REVERT: G 122 TRP cc_start: 0.8248 (m-90) cc_final: 0.7774 (m-10) REVERT: G 162 TYR cc_start: 0.7660 (t80) cc_final: 0.7431 (t80) REVERT: G 344 MET cc_start: 0.7012 (mtm) cc_final: 0.6566 (mtt) outliers start: 26 outliers final: 20 residues processed: 184 average time/residue: 0.1864 time to fit residues: 48.4901 Evaluate side-chains 178 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 158 time to evaluate : 0.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain B residue 96 SER Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 321 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 82 optimal weight: 0.9980 chunk 56 optimal weight: 0.4980 chunk 1 optimal weight: 0.0870 chunk 74 optimal weight: 0.8980 chunk 41 optimal weight: 0.3980 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 7.9990 chunk 89 optimal weight: 20.0000 chunk 25 optimal weight: 0.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 262 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.3988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8806 Z= 0.162 Angle : 0.504 6.600 11887 Z= 0.253 Chirality : 0.041 0.144 1367 Planarity : 0.003 0.049 1463 Dihedral : 10.633 117.383 1336 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.89 % Allowed : 21.64 % Favored : 76.47 % 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 (0.26), residues: 1039 helix: 1.52 (0.22), residues: 584 sheet: 0.72 (0.47), residues: 115 loop : -0.87 (0.33), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP F 271 HIS 0.001 0.000 HIS B 69 PHE 0.019 0.001 PHE G 253 TYR 0.019 0.001 TYR G 260 ARG 0.004 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 162 time to evaluate : 0.991 Fit side-chains REVERT: A 15 LYS cc_start: 0.7037 (mttt) cc_final: 0.6447 (mmtp) REVERT: A 167 MET cc_start: 0.8547 (tpp) cc_final: 0.8245 (tpp) REVERT: A 216 TYR cc_start: 0.8449 (m-80) cc_final: 0.8113 (m-80) REVERT: A 239 ARG cc_start: 0.8142 (mtm-85) cc_final: 0.7390 (mtp85) REVERT: B 20 ASN cc_start: 0.8295 (p0) cc_final: 0.7693 (t0) REVERT: B 142 LEU cc_start: 0.8685 (mp) cc_final: 0.8348 (mt) REVERT: B 204 ASN cc_start: 0.8493 (t0) cc_final: 0.8168 (t0) REVERT: F 156 THR cc_start: 0.8340 (p) cc_final: 0.8068 (p) REVERT: G 122 TRP cc_start: 0.8216 (m-90) cc_final: 0.7750 (m-10) REVERT: G 344 MET cc_start: 0.6994 (mtm) cc_final: 0.6546 (mtt) outliers start: 17 outliers final: 13 residues processed: 172 average time/residue: 0.1943 time to fit residues: 46.9562 Evaluate side-chains 170 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 157 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 33 optimal weight: 9.9990 chunk 89 optimal weight: 20.0000 chunk 19 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 99 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN A 204 ASN B 46 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.4183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8806 Z= 0.192 Angle : 0.507 6.571 11887 Z= 0.252 Chirality : 0.041 0.140 1367 Planarity : 0.003 0.049 1463 Dihedral : 10.450 117.167 1336 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.66 % Allowed : 22.42 % Favored : 74.92 % 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: 1.09 (0.26), residues: 1039 helix: 1.66 (0.22), residues: 582 sheet: 0.70 (0.48), residues: 115 loop : -0.89 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 271 HIS 0.002 0.001 HIS A 81 PHE 0.019 0.001 PHE G 253 TYR 0.014 0.001 TYR G 260 ARG 0.004 0.000 ARG F 145 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.010 Fit side-chains REVERT: A 15 LYS cc_start: 0.6950 (mttt) cc_final: 0.6380 (mmtp) REVERT: A 167 MET cc_start: 0.8564 (tpp) cc_final: 0.8306 (tpp) REVERT: A 216 TYR cc_start: 0.8459 (m-80) cc_final: 0.8119 (m-80) REVERT: A 239 ARG cc_start: 0.8153 (mtm-85) cc_final: 0.7395 (mtp85) REVERT: B 20 ASN cc_start: 0.8334 (p0) cc_final: 0.7706 (t0) REVERT: B 142 LEU cc_start: 0.8680 (mp) cc_final: 0.8355 (mt) REVERT: F 156 THR cc_start: 0.8314 (p) cc_final: 0.8034 (p) REVERT: G 122 TRP cc_start: 0.8228 (m-90) cc_final: 0.7731 (m-10) REVERT: G 344 MET cc_start: 0.7075 (mtm) cc_final: 0.6634 (mtt) outliers start: 24 outliers final: 19 residues processed: 178 average time/residue: 0.1974 time to fit residues: 49.1429 Evaluate side-chains 177 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 158 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 46 ASN Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 248 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 96 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 56 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 83 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.4360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8806 Z= 0.284 Angle : 0.550 6.336 11887 Z= 0.275 Chirality : 0.043 0.149 1367 Planarity : 0.004 0.049 1463 Dihedral : 10.477 114.170 1336 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.89 % Allowed : 22.31 % Favored : 74.81 % 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: 1.12 (0.26), residues: 1039 helix: 1.66 (0.22), residues: 582 sheet: 0.80 (0.48), residues: 113 loop : -0.86 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 271 HIS 0.003 0.001 HIS A 81 PHE 0.030 0.002 PHE G 253 TYR 0.015 0.001 TYR G 260 ARG 0.004 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 167 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.7002 (mttt) cc_final: 0.6372 (mmtp) REVERT: A 167 MET cc_start: 0.8593 (tpp) cc_final: 0.8314 (tpp) REVERT: A 216 TYR cc_start: 0.8508 (m-80) cc_final: 0.8179 (m-80) REVERT: A 239 ARG cc_start: 0.8204 (mtm-85) cc_final: 0.7468 (mtp85) REVERT: B 20 ASN cc_start: 0.8499 (p0) cc_final: 0.7813 (t0) REVERT: B 142 LEU cc_start: 0.8695 (mp) cc_final: 0.8442 (mt) REVERT: F 156 THR cc_start: 0.8327 (p) cc_final: 0.8072 (p) REVERT: G 122 TRP cc_start: 0.8223 (m-90) cc_final: 0.7644 (m-10) REVERT: G 298 GLN cc_start: 0.7599 (OUTLIER) cc_final: 0.6981 (mp10) REVERT: G 344 MET cc_start: 0.7029 (mtm) cc_final: 0.6581 (mtt) outliers start: 26 outliers final: 21 residues processed: 183 average time/residue: 0.1879 time to fit residues: 48.1213 Evaluate side-chains 182 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 160 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 MET Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 191 LEU Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 21 LEU Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 115 ILE Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 134 VAL Chi-restraints excluded: chain G residue 176 ASP Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 39 optimal weight: 0.0970 chunk 59 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 63 optimal weight: 20.0000 chunk 67 optimal weight: 0.0980 chunk 49 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 90 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8806 Z= 0.154 Angle : 0.514 6.868 11887 Z= 0.257 Chirality : 0.040 0.141 1367 Planarity : 0.003 0.047 1463 Dihedral : 10.323 117.686 1336 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 2.44 % Allowed : 23.64 % Favored : 73.92 % 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: 1.29 (0.27), residues: 1039 helix: 1.86 (0.22), residues: 586 sheet: 0.58 (0.48), residues: 117 loop : -0.85 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 271 HIS 0.001 0.000 HIS G 10 PHE 0.026 0.001 PHE G 253 TYR 0.014 0.001 TYR G 260 ARG 0.003 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 172 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 15 LYS cc_start: 0.6974 (mttt) cc_final: 0.6401 (mmtp) REVERT: A 167 MET cc_start: 0.8567 (tpp) cc_final: 0.8323 (tpp) REVERT: A 216 TYR cc_start: 0.8384 (m-80) cc_final: 0.8108 (m-80) REVERT: B 20 ASN cc_start: 0.8432 (p0) cc_final: 0.7784 (t0) REVERT: B 90 TYR cc_start: 0.9087 (t80) cc_final: 0.8864 (t80) REVERT: B 140 ASP cc_start: 0.7891 (m-30) cc_final: 0.7681 (m-30) REVERT: B 142 LEU cc_start: 0.8629 (mp) cc_final: 0.8339 (mt) REVERT: F 156 THR cc_start: 0.8320 (p) cc_final: 0.8059 (p) REVERT: G 122 TRP cc_start: 0.8221 (m-90) cc_final: 0.7682 (m-10) REVERT: G 298 GLN cc_start: 0.7531 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: G 344 MET cc_start: 0.7035 (mtm) cc_final: 0.6588 (mtt) outliers start: 22 outliers final: 15 residues processed: 186 average time/residue: 0.1924 time to fit residues: 50.6032 Evaluate side-chains 175 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 159 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain A residue 203 HIS Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain F residue 2 ILE Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 327 GLU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 86 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 95 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 28 optimal weight: 0.5980 chunk 83 optimal weight: 0.9980 chunk 87 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 97 optimal weight: 0.4980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 41 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8806 Z= 0.225 Angle : 0.545 7.122 11887 Z= 0.271 Chirality : 0.042 0.155 1367 Planarity : 0.004 0.047 1463 Dihedral : 10.316 115.632 1336 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 2.44 % Allowed : 23.86 % Favored : 73.70 % 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: 1.26 (0.27), residues: 1039 helix: 1.82 (0.22), residues: 587 sheet: 0.55 (0.48), residues: 117 loop : -0.82 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 271 HIS 0.003 0.001 HIS F 83 PHE 0.033 0.001 PHE G 253 TYR 0.016 0.001 TYR G 260 ARG 0.008 0.000 ARG G 258 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 162 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.8607 (tpp) cc_final: 0.8323 (tpp) REVERT: A 216 TYR cc_start: 0.8447 (m-80) cc_final: 0.8154 (m-80) REVERT: B 20 ASN cc_start: 0.8469 (p0) cc_final: 0.7804 (t0) REVERT: B 140 ASP cc_start: 0.7933 (m-30) cc_final: 0.7678 (m-30) REVERT: B 142 LEU cc_start: 0.8661 (mp) cc_final: 0.8375 (mt) REVERT: F 156 THR cc_start: 0.8329 (p) cc_final: 0.8117 (p) REVERT: G 122 TRP cc_start: 0.8204 (m-90) cc_final: 0.7639 (m-10) REVERT: G 298 GLN cc_start: 0.7560 (OUTLIER) cc_final: 0.6901 (mp10) REVERT: G 344 MET cc_start: 0.7004 (mtm) cc_final: 0.6555 (mtt) outliers start: 22 outliers final: 17 residues processed: 174 average time/residue: 0.1909 time to fit residues: 46.6768 Evaluate side-chains 177 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 159 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain F residue 327 GLU Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 41 ASN Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 263 VAL Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 102 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 63 optimal weight: 20.0000 chunk 50 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7996 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 8806 Z= 0.298 Angle : 0.879 59.199 11887 Z= 0.505 Chirality : 0.044 0.471 1367 Planarity : 0.004 0.083 1463 Dihedral : 10.335 115.606 1336 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.89 % Allowed : 24.53 % Favored : 73.58 % 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: 1.25 (0.27), residues: 1039 helix: 1.81 (0.22), residues: 587 sheet: 0.53 (0.48), residues: 117 loop : -0.82 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 271 HIS 0.003 0.001 HIS A 81 PHE 0.030 0.001 PHE G 253 TYR 0.014 0.001 TYR G 260 ARG 0.009 0.000 ARG A 24 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2078 Ramachandran restraints generated. 1039 Oldfield, 0 Emsley, 1039 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 167 MET cc_start: 0.8607 (tpp) cc_final: 0.8326 (tpp) REVERT: A 216 TYR cc_start: 0.8452 (m-80) cc_final: 0.8155 (m-80) REVERT: B 20 ASN cc_start: 0.8469 (p0) cc_final: 0.7805 (t0) REVERT: B 140 ASP cc_start: 0.7919 (m-30) cc_final: 0.7680 (m-30) REVERT: B 142 LEU cc_start: 0.8663 (mp) cc_final: 0.8376 (mt) REVERT: F 156 THR cc_start: 0.8370 (p) cc_final: 0.8116 (p) REVERT: G 122 TRP cc_start: 0.8207 (m-90) cc_final: 0.7625 (m-10) REVERT: G 298 GLN cc_start: 0.7552 (OUTLIER) cc_final: 0.6904 (mp10) REVERT: G 344 MET cc_start: 0.7008 (mtm) cc_final: 0.6557 (mtt) outliers start: 17 outliers final: 16 residues processed: 169 average time/residue: 0.2003 time to fit residues: 47.6395 Evaluate side-chains 175 residues out of total 903 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 158 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 ASP Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 177 ASP Chi-restraints excluded: chain B residue 183 ASP Chi-restraints excluded: chain B residue 212 CYS Chi-restraints excluded: chain F residue 23 THR Chi-restraints excluded: chain F residue 52 ILE Chi-restraints excluded: chain F residue 73 MET Chi-restraints excluded: chain F residue 111 VAL Chi-restraints excluded: chain F residue 121 THR Chi-restraints excluded: chain F residue 127 GLN Chi-restraints excluded: chain G residue 15 THR Chi-restraints excluded: chain G residue 23 THR Chi-restraints excluded: chain G residue 56 LEU Chi-restraints excluded: chain G residue 66 ILE Chi-restraints excluded: chain G residue 248 SER Chi-restraints excluded: chain G residue 298 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 103 random chunks: chunk 25 optimal weight: 10.0000 chunk 75 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 chunk 22 optimal weight: 6.9990 chunk 81 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.0270 chunk 15 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 overall best weight: 0.5638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 46 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 131 ASN ** B 106 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 135 GLN ** G 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.121761 restraints weight = 10921.873| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 2.54 r_work: 0.3312 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.4635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 8806 Z= 0.298 Angle : 0.879 59.199 11887 Z= 0.505 Chirality : 0.044 0.471 1367 Planarity : 0.004 0.083 1463 Dihedral : 10.335 115.606 1336 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.89 % Allowed : 24.53 % Favored : 73.58 % 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: 1.25 (0.27), residues: 1039 helix: 1.81 (0.22), residues: 587 sheet: 0.53 (0.48), residues: 117 loop : -0.82 (0.33), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 271 HIS 0.003 0.001 HIS A 81 PHE 0.030 0.001 PHE G 253 TYR 0.014 0.001 TYR G 260 ARG 0.009 0.000 ARG A 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2072.61 seconds wall clock time: 38 minutes 8.28 seconds (2288.28 seconds total)