Starting phenix.real_space_refine on Wed Mar 12 01:48:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn4_33310/03_2025/7xn4_33310.cif" } resolution = 3.35 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= 0.000 sd= 1.000 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 38 5.16 5 C 4335 2.51 5 N 1209 2.21 5 O 1275 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6859 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1706 Classifications: {'peptide': 210} Link IDs: {'PTRANS': 6, 'TRANS': 203} Chain breaks: 2 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1387 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.62, per 1000 atoms: 0.67 Number of scatterers: 6859 At special positions: 0 Unit cell: (110.302, 95.988, 74.096, 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 38 16.00 P 2 15.00 O 1275 8.00 N 1209 7.00 C 4335 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 896.9 milliseconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1602 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 43.4% alpha, 8.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 67 through 82 removed outlier: 3.598A pdb=" N ALA A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LEU A 81 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N LYS A 82 " --> pdb=" O PHE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.528A pdb=" N ILE A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL A 97 " --> pdb=" O ARG A 93 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 105 " --> pdb=" O ARG A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 136 through 142 removed outlier: 3.576A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N PHE A 142 " --> pdb=" O LYS A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 227 removed outlier: 4.298A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA A 227 " --> pdb=" O LEU A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 246 removed outlier: 3.962A pdb=" N ARG A 238 " --> pdb=" O HIS A 234 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 74 removed outlier: 4.025A pdb=" N ILE B 55 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG B 60 " --> pdb=" O GLY B 56 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR B 68 " --> pdb=" O ALA B 64 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 81 Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.729A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASP B 100 " --> pdb=" O LEU B 96 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG B 105 " --> pdb=" O GLY B 101 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU B 114 " --> pdb=" O VAL B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 129 removed outlier: 4.414A pdb=" N ARG B 127 " --> pdb=" O GLY B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 153 through 160 removed outlier: 3.925A pdb=" N GLU B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 224 removed outlier: 3.635A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N HIS B 223 " --> pdb=" O ALA B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 Processing helix chain 'B' and resid 256 through 261 removed outlier: 4.538A pdb=" N ARG B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N TRP B 261 " --> pdb=" O GLU B 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 256 through 261' Processing helix chain 'B' and resid 278 through 293 removed outlier: 3.894A pdb=" N VAL B 283 " --> pdb=" O MET B 279 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.680A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.521A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 348 through 353 Processing helix chain 'B' and resid 355 through 363 Processing helix chain 'B' and resid 365 through 378 removed outlier: 3.533A pdb=" N ASP B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 removed outlier: 3.524A pdb=" N GLY B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASN B 391 " --> pdb=" O HIS B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.865A pdb=" N ALA B 400 " --> pdb=" O GLY B 397 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER B 401 " --> pdb=" O ASP B 398 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 397 through 401' Processing helix chain 'B' and resid 409 through 415 removed outlier: 3.620A pdb=" N SER B 415 " --> pdb=" O ASN B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 420 through 429 removed outlier: 3.561A pdb=" N LEU B 424 " --> pdb=" O SER B 420 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 455 removed outlier: 3.677A pdb=" N ASN B 451 " --> pdb=" O THR B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 468 removed outlier: 3.648A pdb=" N ALA B 463 " --> pdb=" O GLU B 459 " (cutoff:3.500A) Processing helix chain 'C' and resid 69 through 81 removed outlier: 3.703A pdb=" N LEU C 81 " --> pdb=" O THR C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 102 removed outlier: 4.354A pdb=" N MET C 100 " --> pdb=" O ILE C 96 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 106 removed outlier: 3.568A pdb=" N GLU C 106 " --> pdb=" O VAL C 103 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 103 through 106' Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.095A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 removed outlier: 3.509A pdb=" N ASN C 141 " --> pdb=" O LYS C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 213 through 227 removed outlier: 3.663A pdb=" N ALA C 227 " --> pdb=" O LEU C 223 " (cutoff:3.500A) Processing helix chain 'C' and resid 231 through 246 removed outlier: 3.520A pdb=" N ALA C 244 " --> pdb=" O ASN C 240 " (cutoff:3.500A) Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 104 through 112 removed outlier: 3.747A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 127 removed outlier: 4.066A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N GLU D 127 " --> pdb=" O GLU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 135 through 142 removed outlier: 4.040A pdb=" N GLU D 140 " --> pdb=" O ASN D 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N PHE D 141 " --> pdb=" O TYR D 138 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N VAL D 142 " --> pdb=" O GLU D 139 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 89 removed outlier: 5.983A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.762A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N CYS A 116 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N GLN A 161 " --> pdb=" O CYS A 116 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N LEU A 118 " --> pdb=" O GLN A 161 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER C 267 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N TYR C 197 " --> pdb=" O CYS C 264 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 226 Processing sheet with id=AA4, first strand: chain 'B' and resid 150 through 152 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 88 removed outlier: 6.739A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LYS C 88 " --> pdb=" O CYS C 47 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ILE C 49 " --> pdb=" O LYS C 88 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.592A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N GLN C 161 " --> pdb=" O CYS C 116 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU C 118 " --> pdb=" O GLN C 161 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 218 hydrogen bonds defined for protein. 615 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.64 Time building geometry restraints manager: 1.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1144 1.29 - 1.42: 1886 1.42 - 1.55: 3903 1.55 - 1.68: 5 1.68 - 1.81: 64 Bond restraints: 7002 Sorted by residual: bond pdb=" CA ASN B 355 " pdb=" C ASN B 355 " ideal model delta sigma weight residual 1.526 1.438 0.087 1.08e-02 8.57e+03 6.53e+01 bond pdb=" CA LYS B 454 " pdb=" C LYS B 454 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.26e-02 6.30e+03 4.09e+01 bond pdb=" C ASN B 443 " pdb=" O ASN B 443 " ideal model delta sigma weight residual 1.235 1.162 0.073 1.26e-02 6.30e+03 3.37e+01 bond pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 1.332 1.253 0.079 1.40e-02 5.10e+03 3.21e+01 bond pdb=" N GLU A 272 " pdb=" CA GLU A 272 " ideal model delta sigma weight residual 1.454 1.389 0.065 1.16e-02 7.43e+03 3.14e+01 ... (remaining 6997 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.38: 9342 3.38 - 6.76: 73 6.76 - 10.14: 10 10.14 - 13.52: 4 13.52 - 16.90: 1 Bond angle restraints: 9430 Sorted by residual: angle pdb=" N GLU D 123 " pdb=" CA GLU D 123 " pdb=" C GLU D 123 " ideal model delta sigma weight residual 112.23 104.22 8.01 1.26e+00 6.30e-01 4.04e+01 angle pdb=" O VAL B 442 " pdb=" C VAL B 442 " pdb=" N ASN B 443 " ideal model delta sigma weight residual 123.03 117.08 5.95 1.05e+00 9.07e-01 3.21e+01 angle pdb=" C ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta sigma weight residual 111.23 103.22 8.01 1.42e+00 4.96e-01 3.18e+01 angle pdb=" O1A NAD B1001 " pdb=" PA NAD B1001 " pdb=" O2A NAD B1001 " ideal model delta sigma weight residual 122.64 105.74 16.90 3.00e+00 1.11e-01 3.17e+01 angle pdb=" N LEU A 230 " pdb=" CA LEU A 230 " pdb=" C LEU A 230 " ideal model delta sigma weight residual 111.81 119.28 -7.47 1.54e+00 4.22e-01 2.35e+01 ... (remaining 9425 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.17: 3659 16.17 - 32.34: 401 32.34 - 48.50: 123 48.50 - 64.67: 22 64.67 - 80.84: 8 Dihedral angle restraints: 4213 sinusoidal: 1731 harmonic: 2482 Sorted by residual: dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -108.59 -14.01 0 2.50e+00 1.60e-01 3.14e+01 dihedral pdb=" CA PRO B 329 " pdb=" C PRO B 329 " pdb=" N ARG B 330 " pdb=" CA ARG B 330 " ideal model delta harmonic sigma weight residual -180.00 -157.54 -22.46 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA GLN B 253 " pdb=" C GLN B 253 " pdb=" N MET B 254 " pdb=" CA MET B 254 " ideal model delta harmonic sigma weight residual 180.00 157.64 22.36 0 5.00e+00 4.00e-02 2.00e+01 ... (remaining 4210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 896 0.065 - 0.131: 99 0.131 - 0.196: 10 0.196 - 0.261: 2 0.261 - 0.326: 2 Chirality restraints: 1009 Sorted by residual: chirality pdb=" CA ASN B 443 " pdb=" N ASN B 443 " pdb=" C ASN B 443 " pdb=" CB ASN B 443 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" C2B NAD B1001 " pdb=" C1B NAD B1001 " pdb=" C3B NAD B1001 " pdb=" O2B NAD B1001 " both_signs ideal model delta sigma weight residual False -2.53 -2.84 0.31 2.00e-01 2.50e+01 2.33e+00 chirality pdb=" CA GLN B 66 " pdb=" N GLN B 66 " pdb=" C GLN B 66 " pdb=" CB GLN B 66 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.53e+00 ... (remaining 1006 not shown) Planarity restraints: 1218 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 442 " 0.025 2.00e-02 2.50e+03 4.77e-02 2.28e+01 pdb=" C VAL B 442 " -0.083 2.00e-02 2.50e+03 pdb=" O VAL B 442 " 0.029 2.00e-02 2.50e+03 pdb=" N ASN B 443 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG D 126 " 0.018 2.00e-02 2.50e+03 3.70e-02 1.37e+01 pdb=" C ARG D 126 " -0.064 2.00e-02 2.50e+03 pdb=" O ARG D 126 " 0.024 2.00e-02 2.50e+03 pdb=" N GLU D 127 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 122 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C ASP D 122 " -0.051 2.00e-02 2.50e+03 pdb=" O ASP D 122 " 0.019 2.00e-02 2.50e+03 pdb=" N GLU D 123 " 0.017 2.00e-02 2.50e+03 ... (remaining 1215 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1142 2.76 - 3.29: 6485 3.29 - 3.83: 10573 3.83 - 4.36: 13299 4.36 - 4.90: 22625 Nonbonded interactions: 54124 Sorted by model distance: nonbonded pdb=" NE2 GLN B 253 " pdb=" O LYS B 295 " model vdw 2.223 3.120 nonbonded pdb=" O2B NAD B1001 " pdb=" O3B NAD B1001 " model vdw 2.261 2.432 nonbonded pdb=" O GLY B 171 " pdb=" N LEU B 175 " model vdw 2.275 3.120 nonbonded pdb=" OD1 ASN D 97 " pdb=" N GLY D 98 " model vdw 2.279 3.120 nonbonded pdb=" OG SER B 429 " pdb=" ND1 HIS B 467 " model vdw 2.296 3.120 ... (remaining 54119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 3.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 18.980 Find NCS groups from input model: 0.060 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: 0.000 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: 25.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 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 : 0.005 0.102 7002 Z= 0.359 Angle : 0.795 16.897 9430 Z= 0.404 Chirality : 0.047 0.326 1009 Planarity : 0.005 0.068 1218 Dihedral : 15.383 80.840 2611 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.70 % Allowed : 0.70 % Favored : 98.60 % Cbeta Deviations : 0.12 % 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: -2.93 (0.28), residues: 837 helix: -1.71 (0.26), residues: 305 sheet: -2.94 (0.48), residues: 115 loop : -1.72 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 214 HIS 0.005 0.001 HIS B 202 PHE 0.020 0.001 PHE B 233 TYR 0.022 0.001 TYR A 37 ARG 0.006 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 150 time to evaluate : 0.767 Fit side-chains REVERT: A 102 ASP cc_start: 0.7355 (m-30) cc_final: 0.7034 (m-30) REVERT: A 135 ASP cc_start: 0.6982 (p0) cc_final: 0.6333 (t70) REVERT: C 107 ASP cc_start: 0.7442 (t70) cc_final: 0.7105 (t0) REVERT: D 85 ILE cc_start: 0.8045 (pt) cc_final: 0.7838 (mt) REVERT: D 130 ILE cc_start: 0.5948 (mm) cc_final: 0.5373 (tp) outliers start: 5 outliers final: 0 residues processed: 152 average time/residue: 0.2088 time to fit residues: 41.7255 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 125 time to evaluate : 0.844 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 65 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.0980 chunk 49 optimal weight: 0.8980 chunk 76 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS B 244 HIS C 80 ASN C 161 GLN D 107 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.141893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.115206 restraints weight = 11464.557| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.58 r_work: 0.3435 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.213 Angle : 0.621 14.171 9430 Z= 0.317 Chirality : 0.043 0.179 1009 Planarity : 0.005 0.049 1218 Dihedral : 7.322 50.382 988 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 0.98 % Allowed : 8.39 % Favored : 90.63 % 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: -2.53 (0.28), residues: 837 helix: -1.11 (0.27), residues: 313 sheet: -2.79 (0.44), residues: 129 loop : -1.65 (0.32), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 214 HIS 0.017 0.001 HIS A 121 PHE 0.011 0.001 PHE B 233 TYR 0.017 0.001 TYR D 99 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.804 Fit side-chains REVERT: A 102 ASP cc_start: 0.7689 (m-30) cc_final: 0.7266 (m-30) REVERT: A 135 ASP cc_start: 0.7201 (p0) cc_final: 0.6593 (t70) REVERT: B 302 TYR cc_start: 0.6629 (OUTLIER) cc_final: 0.5850 (t80) REVERT: B 448 MET cc_start: 0.8153 (mtt) cc_final: 0.7857 (mtt) REVERT: C 240 ASN cc_start: 0.8468 (t0) cc_final: 0.8249 (t0) outliers start: 7 outliers final: 1 residues processed: 137 average time/residue: 0.2006 time to fit residues: 36.4292 Evaluate side-chains 125 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 53 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 80 ASN D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3868 r_free = 0.3868 target = 0.138340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.110825 restraints weight = 11342.985| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 2.63 r_work: 0.3352 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 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 : 0.004 0.042 7002 Z= 0.265 Angle : 0.606 9.266 9430 Z= 0.314 Chirality : 0.043 0.167 1009 Planarity : 0.005 0.052 1218 Dihedral : 7.121 59.380 988 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.26 % Allowed : 11.75 % Favored : 86.99 % 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: -2.61 (0.28), residues: 837 helix: -0.98 (0.27), residues: 324 sheet: -2.78 (0.44), residues: 127 loop : -1.93 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.006 0.001 HIS B 202 PHE 0.015 0.001 PHE B 78 TYR 0.012 0.001 TYR B 225 ARG 0.003 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 128 time to evaluate : 0.802 Fit side-chains REVERT: A 102 ASP cc_start: 0.7742 (m-30) cc_final: 0.7327 (m-30) REVERT: A 135 ASP cc_start: 0.7327 (p0) cc_final: 0.6716 (t70) REVERT: A 225 GLN cc_start: 0.8258 (pm20) cc_final: 0.7905 (pm20) REVERT: B 302 TYR cc_start: 0.6597 (OUTLIER) cc_final: 0.5827 (t80) REVERT: B 448 MET cc_start: 0.8502 (mtt) cc_final: 0.8301 (mtt) outliers start: 9 outliers final: 4 residues processed: 133 average time/residue: 0.1755 time to fit residues: 31.9431 Evaluate side-chains 126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 121 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 35 optimal weight: 0.0040 chunk 14 optimal weight: 0.0670 chunk 63 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 78 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 79 optimal weight: 0.7980 overall best weight: 0.4530 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.142788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.115826 restraints weight = 11410.896| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 2.59 r_work: 0.3451 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7002 Z= 0.167 Angle : 0.568 16.423 9430 Z= 0.287 Chirality : 0.041 0.153 1009 Planarity : 0.004 0.051 1218 Dihedral : 6.548 59.512 988 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 1.40 % Allowed : 14.55 % Favored : 84.06 % 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: -2.34 (0.28), residues: 837 helix: -0.72 (0.28), residues: 328 sheet: -2.56 (0.45), residues: 127 loop : -1.85 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 206 HIS 0.006 0.001 HIS A 121 PHE 0.011 0.001 PHE B 299 TYR 0.009 0.001 TYR B 225 ARG 0.002 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 127 time to evaluate : 0.788 Fit side-chains REVERT: A 102 ASP cc_start: 0.7746 (m-30) cc_final: 0.7344 (m-30) REVERT: A 135 ASP cc_start: 0.7212 (p0) cc_final: 0.6709 (t70) REVERT: A 225 GLN cc_start: 0.8193 (pm20) cc_final: 0.7911 (pm20) REVERT: B 167 ASN cc_start: 0.7791 (m-40) cc_final: 0.7547 (m110) REVERT: B 302 TYR cc_start: 0.6458 (OUTLIER) cc_final: 0.5715 (t80) REVERT: C 70 ASP cc_start: 0.8512 (p0) cc_final: 0.8117 (p0) outliers start: 10 outliers final: 6 residues processed: 131 average time/residue: 0.1750 time to fit residues: 31.1328 Evaluate side-chains 130 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 123 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 26 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 64 optimal weight: 0.4980 chunk 2 optimal weight: 0.2980 chunk 17 optimal weight: 0.2980 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3913 r_free = 0.3913 target = 0.141858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.113485 restraints weight = 11380.828| |-----------------------------------------------------------------------------| r_work (start): 0.3534 rms_B_bonded: 2.72 r_work: 0.3387 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.175 Angle : 0.553 13.084 9430 Z= 0.283 Chirality : 0.041 0.157 1009 Planarity : 0.004 0.052 1218 Dihedral : 6.249 54.675 988 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.36 % Favored : 91.64 % Rotamer: Outliers : 1.54 % Allowed : 15.52 % Favored : 82.94 % 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: -2.23 (0.29), residues: 837 helix: -0.61 (0.28), residues: 328 sheet: -2.48 (0.45), residues: 127 loop : -1.81 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 261 HIS 0.005 0.001 HIS A 121 PHE 0.012 0.001 PHE B 233 TYR 0.010 0.001 TYR B 225 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 127 time to evaluate : 0.815 Fit side-chains REVERT: A 102 ASP cc_start: 0.7774 (m-30) cc_final: 0.7377 (m-30) REVERT: A 135 ASP cc_start: 0.7305 (p0) cc_final: 0.6769 (t70) REVERT: A 225 GLN cc_start: 0.8192 (pm20) cc_final: 0.7926 (pm20) REVERT: B 167 ASN cc_start: 0.7718 (m-40) cc_final: 0.7438 (m110) REVERT: B 302 TYR cc_start: 0.6453 (OUTLIER) cc_final: 0.5831 (t80) REVERT: C 70 ASP cc_start: 0.8580 (p0) cc_final: 0.8171 (p0) outliers start: 11 outliers final: 6 residues processed: 132 average time/residue: 0.1771 time to fit residues: 32.0545 Evaluate side-chains 128 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 121 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 32 optimal weight: 0.0370 chunk 43 optimal weight: 0.5980 chunk 68 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 64 optimal weight: 0.2980 chunk 27 optimal weight: 3.9990 overall best weight: 0.3858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.143135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.114776 restraints weight = 11422.078| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 2.74 r_work: 0.3417 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7002 Z= 0.157 Angle : 0.559 15.062 9430 Z= 0.281 Chirality : 0.040 0.154 1009 Planarity : 0.004 0.052 1218 Dihedral : 5.928 49.810 988 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 1.54 % Allowed : 17.20 % Favored : 81.26 % 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: -2.04 (0.29), residues: 837 helix: -0.45 (0.29), residues: 331 sheet: -2.37 (0.45), residues: 127 loop : -1.72 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 261 HIS 0.004 0.001 HIS A 121 PHE 0.015 0.001 PHE B 233 TYR 0.011 0.001 TYR D 138 ARG 0.002 0.000 ARG B 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 131 time to evaluate : 0.633 Fit side-chains REVERT: A 102 ASP cc_start: 0.7789 (m-30) cc_final: 0.7403 (m-30) REVERT: A 135 ASP cc_start: 0.7180 (p0) cc_final: 0.6723 (t70) REVERT: A 225 GLN cc_start: 0.8199 (pm20) cc_final: 0.7973 (pm20) REVERT: B 122 ARG cc_start: 0.8499 (mmp80) cc_final: 0.8254 (mmp-170) REVERT: B 167 ASN cc_start: 0.7703 (m-40) cc_final: 0.7430 (m110) REVERT: B 302 TYR cc_start: 0.6435 (OUTLIER) cc_final: 0.5843 (t80) REVERT: B 336 ASP cc_start: 0.8222 (t0) cc_final: 0.7900 (t0) REVERT: B 448 MET cc_start: 0.7986 (mtt) cc_final: 0.7731 (mtt) REVERT: C 70 ASP cc_start: 0.8579 (p0) cc_final: 0.8169 (p0) REVERT: D 97 ASN cc_start: 0.8077 (t0) cc_final: 0.7856 (t0) outliers start: 11 outliers final: 7 residues processed: 136 average time/residue: 0.1698 time to fit residues: 31.4360 Evaluate side-chains 127 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 119 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 54 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 50 optimal weight: 6.9990 chunk 6 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 24 optimal weight: 0.0770 chunk 44 optimal weight: 0.6980 chunk 10 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.7544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.136951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.110726 restraints weight = 11489.019| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.53 r_work: 0.3364 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 7002 Z= 0.391 Angle : 0.687 12.014 9430 Z= 0.351 Chirality : 0.046 0.208 1009 Planarity : 0.005 0.054 1218 Dihedral : 6.825 45.747 988 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.92 % Favored : 90.08 % Rotamer: Outliers : 1.82 % Allowed : 18.04 % Favored : 80.14 % 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: -2.46 (0.28), residues: 837 helix: -0.75 (0.28), residues: 326 sheet: -2.66 (0.43), residues: 130 loop : -1.95 (0.32), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 432 HIS 0.008 0.001 HIS B 202 PHE 0.019 0.002 PHE B 78 TYR 0.013 0.002 TYR B 225 ARG 0.003 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 121 time to evaluate : 0.779 Fit side-chains REVERT: A 102 ASP cc_start: 0.7735 (m-30) cc_final: 0.7339 (m-30) REVERT: B 302 TYR cc_start: 0.6668 (OUTLIER) cc_final: 0.5677 (t80) REVERT: B 308 MET cc_start: 0.8462 (OUTLIER) cc_final: 0.8237 (ptt) REVERT: C 157 LEU cc_start: 0.9223 (OUTLIER) cc_final: 0.9005 (mt) REVERT: D 97 ASN cc_start: 0.8042 (t0) cc_final: 0.7793 (t0) REVERT: D 139 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7983 (mm-30) outliers start: 13 outliers final: 6 residues processed: 126 average time/residue: 0.1796 time to fit residues: 31.0744 Evaluate side-chains 126 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 117 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 308 MET Chi-restraints excluded: chain B residue 449 LEU Chi-restraints excluded: chain C residue 157 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 33 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 34 optimal weight: 0.2980 chunk 58 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.114398 restraints weight = 11372.886| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.59 r_work: 0.3425 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7002 Z= 0.200 Angle : 0.618 16.069 9430 Z= 0.310 Chirality : 0.042 0.187 1009 Planarity : 0.004 0.052 1218 Dihedral : 6.372 52.692 988 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.24 % Favored : 91.76 % Rotamer: Outliers : 1.54 % Allowed : 18.88 % Favored : 79.58 % 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: -2.20 (0.29), residues: 837 helix: -0.52 (0.29), residues: 327 sheet: -2.53 (0.44), residues: 127 loop : -1.84 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 214 HIS 0.008 0.001 HIS A 121 PHE 0.017 0.001 PHE B 233 TYR 0.012 0.001 TYR D 138 ARG 0.002 0.000 ARG C 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 128 time to evaluate : 0.814 Fit side-chains REVERT: A 102 ASP cc_start: 0.7731 (m-30) cc_final: 0.7328 (m-30) REVERT: A 135 ASP cc_start: 0.6803 (p0) cc_final: 0.6241 (t70) REVERT: B 167 ASN cc_start: 0.7871 (m-40) cc_final: 0.7606 (m110) REVERT: B 302 TYR cc_start: 0.6483 (OUTLIER) cc_final: 0.5559 (t80) REVERT: B 336 ASP cc_start: 0.8188 (t0) cc_final: 0.7903 (t0) REVERT: D 97 ASN cc_start: 0.7976 (t0) cc_final: 0.7704 (t0) REVERT: D 112 LEU cc_start: 0.8473 (mt) cc_final: 0.8224 (mt) outliers start: 11 outliers final: 6 residues processed: 132 average time/residue: 0.1939 time to fit residues: 35.4458 Evaluate side-chains 132 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 125 time to evaluate : 0.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 31 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 49 optimal weight: 0.7980 chunk 68 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 70 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN D 107 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.140823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.113775 restraints weight = 11558.396| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.60 r_work: 0.3410 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.223 Angle : 0.621 14.985 9430 Z= 0.312 Chirality : 0.042 0.181 1009 Planarity : 0.004 0.052 1218 Dihedral : 6.326 53.452 988 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.40 % Allowed : 19.02 % Favored : 79.58 % 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: -2.15 (0.29), residues: 837 helix: -0.48 (0.29), residues: 327 sheet: -2.54 (0.43), residues: 127 loop : -1.80 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 261 HIS 0.010 0.001 HIS A 121 PHE 0.011 0.001 PHE B 78 TYR 0.012 0.001 TYR D 138 ARG 0.002 0.000 ARG B 127 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.725 Fit side-chains REVERT: A 102 ASP cc_start: 0.7746 (m-30) cc_final: 0.7393 (m-30) REVERT: A 135 ASP cc_start: 0.6834 (p0) cc_final: 0.6267 (t70) REVERT: B 302 TYR cc_start: 0.6466 (OUTLIER) cc_final: 0.5632 (t80) REVERT: D 97 ASN cc_start: 0.7976 (t0) cc_final: 0.7689 (t0) REVERT: D 112 LEU cc_start: 0.8512 (mt) cc_final: 0.8267 (mt) outliers start: 10 outliers final: 8 residues processed: 130 average time/residue: 0.1775 time to fit residues: 31.5626 Evaluate side-chains 129 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain A residue 261 GLN Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 0.7980 chunk 25 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 43 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 overall best weight: 0.8720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3910 r_free = 0.3910 target = 0.140673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.113506 restraints weight = 11665.063| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.62 r_work: 0.3409 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.2310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 7002 Z= 0.234 Angle : 0.633 16.351 9430 Z= 0.319 Chirality : 0.042 0.177 1009 Planarity : 0.004 0.053 1218 Dihedral : 6.360 54.124 988 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.96 % Favored : 91.04 % Rotamer: Outliers : 1.40 % Allowed : 19.30 % Favored : 79.30 % 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: -2.16 (0.29), residues: 837 helix: -0.49 (0.29), residues: 328 sheet: -2.56 (0.43), residues: 127 loop : -1.80 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 214 HIS 0.011 0.001 HIS A 121 PHE 0.012 0.001 PHE B 78 TYR 0.013 0.001 TYR D 138 ARG 0.003 0.000 ARG B 122 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 123 time to evaluate : 0.784 Fit side-chains REVERT: A 102 ASP cc_start: 0.7743 (m-30) cc_final: 0.7386 (m-30) REVERT: A 135 ASP cc_start: 0.6802 (p0) cc_final: 0.6229 (t70) REVERT: B 302 TYR cc_start: 0.6446 (OUTLIER) cc_final: 0.5603 (t80) REVERT: B 449 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8543 (mt) REVERT: D 97 ASN cc_start: 0.7980 (t0) cc_final: 0.7697 (t0) REVERT: D 112 LEU cc_start: 0.8493 (mt) cc_final: 0.8273 (mt) outliers start: 10 outliers final: 7 residues processed: 127 average time/residue: 0.1744 time to fit residues: 30.2183 Evaluate side-chains 128 residues out of total 715 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 119 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 ASP Chi-restraints excluded: chain A residue 99 LEU Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 189 VAL Chi-restraints excluded: chain A residue 223 LEU Chi-restraints excluded: chain A residue 226 TYR Chi-restraints excluded: chain B residue 55 ILE Chi-restraints excluded: chain B residue 302 TYR Chi-restraints excluded: chain B residue 449 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 58 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 2 optimal weight: 0.0770 chunk 59 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 36 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 261 GLN ** B 234 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 161 GLN D 107 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.141554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.114447 restraints weight = 11591.190| |-----------------------------------------------------------------------------| r_work (start): 0.3567 rms_B_bonded: 2.61 r_work: 0.3428 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7002 Z= 0.202 Angle : 0.614 16.002 9430 Z= 0.310 Chirality : 0.041 0.174 1009 Planarity : 0.004 0.052 1218 Dihedral : 6.237 55.397 988 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % Rotamer: Outliers : 1.26 % Allowed : 19.16 % Favored : 79.58 % 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: -2.04 (0.29), residues: 837 helix: -0.37 (0.29), residues: 328 sheet: -2.50 (0.44), residues: 127 loop : -1.74 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 214 HIS 0.004 0.001 HIS B 202 PHE 0.010 0.001 PHE B 233 TYR 0.011 0.001 TYR D 138 ARG 0.002 0.000 ARG B 122 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3312.50 seconds wall clock time: 57 minutes 40.65 seconds (3460.65 seconds total)