Starting phenix.real_space_refine on Sun Jan 26 12:32:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.map" model { file = "/net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ljo_4061/01_2025/5ljo_4061.cif" } resolution = 4.9 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= 0.008 sd= 0.058 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 S 33 5.16 5 C 7986 2.51 5 N 2172 2.21 5 O 2501 1.98 5 H 12255 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 68 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 24947 Number of models: 1 Model: "" Number of chains: 5 Chain: "B" Number of atoms: 5534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 5534 Classifications: {'peptide': 371} Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 357} Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 2498 Classifications: {'peptide': 165} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 153} Chain: "D" Number of atoms: 3461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 3461 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 12, 'TRANS': 205} Chain: "E" Number of atoms: 1352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1352 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 5, 'TRANS': 81} Chain: "A" Number of atoms: 12102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 783, 12102 Classifications: {'peptide': 783} Link IDs: {'CIS': 2, 'PTRANS': 29, 'TRANS': 751} Time building chain proxies: 11.12, per 1000 atoms: 0.45 Number of scatterers: 24947 At special positions: 0 Unit cell: (137.28, 115.44, 138.32, 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 33 16.00 O 2501 8.00 N 2172 7.00 C 7986 6.00 H 12255 1.00 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: 6.79 Conformation dependent library (CDL) restraints added in 2.0 seconds 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2972 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 20 sheets defined 24.6% alpha, 27.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.15 Creating SS restraints... Processing helix chain 'B' and resid 22 through 27 Processing helix chain 'C' and resid 39 through 44 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 115 through 128 Processing helix chain 'D' and resid 31 through 46 Processing helix chain 'D' and resid 47 through 62 Processing helix chain 'D' and resid 67 through 82 Processing helix chain 'D' and resid 84 through 99 Processing helix chain 'D' and resid 104 through 121 Processing helix chain 'D' and resid 123 through 129 Processing helix chain 'D' and resid 137 through 154 Processing helix chain 'D' and resid 159 through 189 Processing helix chain 'D' and resid 190 through 205 Processing helix chain 'D' and resid 208 through 225 Proline residue: D 216 - end of helix Processing helix chain 'D' and resid 227 through 241 Processing helix chain 'E' and resid 39 through 45 Processing helix chain 'E' and resid 51 through 60 removed outlier: 4.728A pdb=" N ALA E 58 " --> pdb=" O GLN E 54 " (cutoff:3.500A) Processing helix chain 'A' and resid 38 through 46 Processing helix chain 'A' and resid 55 through 68 Processing helix chain 'A' and resid 106 through 117 Processing helix chain 'A' and resid 126 through 128 No H-bonds generated for 'chain 'A' and resid 126 through 128' Processing helix chain 'A' and resid 129 through 145 Processing helix chain 'A' and resid 159 through 161 No H-bonds generated for 'chain 'A' and resid 159 through 161' Processing helix chain 'A' and resid 189 through 195 Processing helix chain 'A' and resid 204 through 208 removed outlier: 4.081A pdb=" N VAL A 208 " --> pdb=" O TRP A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 232 Processing helix chain 'A' and resid 280 through 288 Processing helix chain 'A' and resid 297 through 315 Processing helix chain 'A' and resid 362 through 367 Processing helix chain 'A' and resid 378 through 393 removed outlier: 4.356A pdb=" N GLY A 393 " --> pdb=" O LEU A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 452 Processing helix chain 'A' and resid 542 through 552 Processing helix chain 'A' and resid 647 through 651 Processing helix chain 'A' and resid 726 through 731 Processing sheet with id=AA1, first strand: chain 'B' and resid 45 through 48 removed outlier: 4.604A pdb=" N THR B 46 " --> pdb=" O THR B 391 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N THR B 391 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 66 through 68 removed outlier: 6.121A pdb=" N ASN B 85 " --> pdb=" O GLU B 91 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N GLU B 91 " --> pdb=" O ASN B 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 116 through 118 removed outlier: 6.272A pdb=" N ASN B 135 " --> pdb=" O VAL B 141 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N VAL B 141 " --> pdb=" O ASN B 135 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 156 through 158 removed outlier: 6.032A pdb=" N LEU B 171 " --> pdb=" O THR B 184 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N THR B 184 " --> pdb=" O LEU B 171 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N ALA B 173 " --> pdb=" O LYS B 182 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 194 removed outlier: 7.100A pdb=" N SER B 193 " --> pdb=" O LEU A 247 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ILE A 240 " --> pdb=" O THR A 261 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N THR A 261 " --> pdb=" O ILE A 240 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N TYR A 255 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N VAL A 256 " --> pdb=" O GLN A 178 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ILE A 180 " --> pdb=" O VAL A 256 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N VAL A 258 " --> pdb=" O ILE A 180 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE A 182 " --> pdb=" O VAL A 258 " (cutoff:3.500A) removed outlier: 7.299A pdb=" N ILE A 260 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 201 through 203 removed outlier: 5.495A pdb=" N LEU B 220 " --> pdb=" O MET B 226 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N MET B 226 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 252 through 254 removed outlier: 6.372A pdb=" N ASP B 271 " --> pdb=" O ILE B 277 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE B 277 " --> pdb=" O ASP B 271 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 288 through 292 removed outlier: 6.500A pdb=" N VAL B 305 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N THR B 318 " --> pdb=" O VAL B 305 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ALA B 307 " --> pdb=" O LEU B 316 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 331 through 333 removed outlier: 6.497A pdb=" N LEU B 346 " --> pdb=" O GLN B 359 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N GLN B 359 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N TRP B 348 " --> pdb=" O VAL B 357 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 98 through 100 removed outlier: 6.067A pdb=" N VAL C 174 " --> pdb=" O LYS C 166 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N LYS C 166 " --> pdb=" O VAL C 174 " (cutoff:3.500A) removed outlier: 5.668A pdb=" N VAL C 176 " --> pdb=" O SER C 164 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N SER C 164 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU C 178 " --> pdb=" O GLN C 162 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N GLN C 162 " --> pdb=" O LEU C 178 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N TYR C 161 " --> pdb=" O ASP C 144 " (cutoff:3.500A) removed outlier: 5.400A pdb=" N ASP C 144 " --> pdb=" O TYR C 161 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE C 163 " --> pdb=" O THR C 142 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N THR C 142 " --> pdb=" O ILE C 163 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL C 165 " --> pdb=" O THR C 140 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N THR C 140 " --> pdb=" O VAL C 165 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ASP C 144 " --> pdb=" O ILE C 131 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ILE C 131 " --> pdb=" O ASP C 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 108 through 109 removed outlier: 4.440A pdb=" N LEU C 181 " --> pdb=" O VAL C 188 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 73 through 79 removed outlier: 5.982A pdb=" N THR E 90 " --> pdb=" O ASN E 106 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N ASN E 106 " --> pdb=" O THR E 90 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N THR E 92 " --> pdb=" O ILE E 104 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ILE E 104 " --> pdb=" O THR E 92 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N THR E 94 " --> pdb=" O THR E 102 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 29 through 31 Processing sheet with id=AB5, first strand: chain 'A' and resid 72 through 74 Processing sheet with id=AB6, first strand: chain 'A' and resid 94 through 100 removed outlier: 4.626A pdb=" N ILE A 94 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N LEU A 165 " --> pdb=" O ILE A 94 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N SER A 96 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N LEU A 167 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N THR A 98 " --> pdb=" O LEU A 167 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N PHE A 169 " --> pdb=" O THR A 98 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N SER A 100 " --> pdb=" O PHE A 169 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 171 " --> pdb=" O SER A 100 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N SER A 148 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N SER A 174 " --> pdb=" O LYS A 146 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LYS A 146 " --> pdb=" O SER A 174 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 294 through 295 removed outlier: 5.684A pdb=" N VAL A 335 " --> pdb=" O LEU A 268 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 349 through 355 removed outlier: 4.739A pdb=" N VAL A 349 " --> pdb=" O VAL A 412 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N VAL A 414 " --> pdb=" O VAL A 349 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N LYS A 351 " --> pdb=" O VAL A 414 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N TYR A 416 " --> pdb=" O LYS A 351 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ARG A 353 " --> pdb=" O TYR A 416 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 395 through 397 removed outlier: 6.409A pdb=" N LYS A 419 " --> pdb=" O GLU A 396 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 425 through 426 removed outlier: 3.564A pdb=" N SER A 472 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N PHE A 494 " --> pdb=" O ASN A 506 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N TYR A 608 " --> pdb=" O THR A 600 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 735 " --> pdb=" O THR A 720 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 662 through 663 removed outlier: 4.189A pdb=" N GLY A 662 " --> pdb=" O GLU A 800 " (cutoff:3.500A) 563 hydrogen bonds defined for protein. 1542 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: 10.54 Time building geometry restraints manager: 7.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.95 - 1.12: 12252 1.12 - 1.29: 2199 1.29 - 1.47: 5190 1.47 - 1.64: 5516 1.64 - 1.81: 63 Bond restraints: 25220 Sorted by residual: bond pdb=" CE1 TYR A 688 " pdb=" HE1 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.76e+01 bond pdb=" CD2 TYR A 688 " pdb=" HD2 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.74e+01 bond pdb=" CD1 TYR A 688 " pdb=" HD1 TYR A 688 " ideal model delta sigma weight residual 0.930 1.094 -0.164 2.00e-02 2.50e+03 6.72e+01 bond pdb=" CE2 TYR A 688 " pdb=" HE2 TYR A 688 " ideal model delta sigma weight residual 0.930 1.093 -0.163 2.00e-02 2.50e+03 6.61e+01 bond pdb=" N GLU A 645 " pdb=" H GLU A 645 " ideal model delta sigma weight residual 0.860 1.022 -0.162 2.00e-02 2.50e+03 6.57e+01 ... (remaining 25215 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.84: 40323 2.84 - 5.68: 3983 5.68 - 8.52: 1005 8.52 - 11.37: 43 11.37 - 14.21: 8 Bond angle restraints: 45362 Sorted by residual: angle pdb=" CA PHE A 395 " pdb=" CB PHE A 395 " pdb=" CG PHE A 395 " ideal model delta sigma weight residual 113.80 104.92 8.88 1.00e+00 1.00e+00 7.88e+01 angle pdb=" C TYR D 62 " pdb=" N PRO D 63 " pdb=" CA PRO D 63 " ideal model delta sigma weight residual 119.56 128.48 -8.92 1.02e+00 9.61e-01 7.65e+01 angle pdb=" C ASP A 762 " pdb=" N PRO A 763 " pdb=" CA PRO A 763 " ideal model delta sigma weight residual 119.82 128.29 -8.47 9.80e-01 1.04e+00 7.47e+01 angle pdb=" C ALA C 45 " pdb=" N PRO C 46 " pdb=" CA PRO C 46 " ideal model delta sigma weight residual 120.03 128.51 -8.48 9.90e-01 1.02e+00 7.34e+01 angle pdb=" C GLY A 781 " pdb=" N PRO A 782 " pdb=" CA PRO A 782 " ideal model delta sigma weight residual 119.98 129.87 -9.89 1.16e+00 7.43e-01 7.26e+01 ... (remaining 45357 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.65: 11310 17.65 - 35.31: 417 35.31 - 52.96: 159 52.96 - 70.62: 55 70.62 - 88.27: 16 Dihedral angle restraints: 11957 sinusoidal: 6453 harmonic: 5504 Sorted by residual: dihedral pdb=" CA ASP B 353 " pdb=" C ASP B 353 " pdb=" N GLY B 354 " pdb=" CA GLY B 354 " ideal model delta harmonic sigma weight residual 0.00 41.47 -41.47 0 5.00e+00 4.00e-02 6.88e+01 dihedral pdb=" CA PRO A 92 " pdb=" C PRO A 92 " pdb=" N THR A 93 " pdb=" CA THR A 93 " ideal model delta harmonic sigma weight residual 0.00 -37.88 37.88 0 5.00e+00 4.00e-02 5.74e+01 dihedral pdb=" CA SER B 54 " pdb=" C SER B 54 " pdb=" N GLY B 55 " pdb=" CA GLY B 55 " ideal model delta harmonic sigma weight residual 0.00 -37.30 37.30 0 5.00e+00 4.00e-02 5.57e+01 ... (remaining 11954 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1229 0.069 - 0.137: 556 0.137 - 0.206: 125 0.206 - 0.275: 10 0.275 - 0.343: 9 Chirality restraints: 1929 Sorted by residual: chirality pdb=" CA PHE D 169 " pdb=" N PHE D 169 " pdb=" C PHE D 169 " pdb=" CB PHE D 169 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.94e+00 chirality pdb=" CA PHE A 738 " pdb=" N PHE A 738 " pdb=" C PHE A 738 " pdb=" CB PHE A 738 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.40e+00 chirality pdb=" CA ARG A 162 " pdb=" N ARG A 162 " pdb=" C ARG A 162 " pdb=" CB ARG A 162 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1926 not shown) Planarity restraints: 3878 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 533 " -0.105 2.00e-02 2.50e+03 1.11e-01 2.78e+02 pdb=" CG HIS A 533 " -0.058 2.00e-02 2.50e+03 pdb=" ND1 HIS A 533 " -0.101 2.00e-02 2.50e+03 pdb=" CD2 HIS A 533 " 0.027 2.00e-02 2.50e+03 pdb=" CE1 HIS A 533 " -0.056 2.00e-02 2.50e+03 pdb=" NE2 HIS A 533 " 0.025 2.00e-02 2.50e+03 pdb=" HD1 HIS A 533 " 0.259 2.00e-02 2.50e+03 pdb=" HD2 HIS A 533 " 0.091 2.00e-02 2.50e+03 pdb=" HE1 HIS A 533 " -0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS A 625 " -0.082 2.00e-02 2.50e+03 8.70e-02 1.70e+02 pdb=" CG HIS A 625 " -0.043 2.00e-02 2.50e+03 pdb=" ND1 HIS A 625 " -0.086 2.00e-02 2.50e+03 pdb=" CD2 HIS A 625 " 0.021 2.00e-02 2.50e+03 pdb=" CE1 HIS A 625 " -0.043 2.00e-02 2.50e+03 pdb=" NE2 HIS A 625 " 0.022 2.00e-02 2.50e+03 pdb=" HD1 HIS A 625 " 0.202 2.00e-02 2.50e+03 pdb=" HD2 HIS A 625 " 0.069 2.00e-02 2.50e+03 pdb=" HE1 HIS A 625 " -0.061 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 92 " -0.063 2.00e-02 2.50e+03 1.28e-01 1.65e+02 pdb=" C PRO A 92 " 0.222 2.00e-02 2.50e+03 pdb=" O PRO A 92 " -0.082 2.00e-02 2.50e+03 pdb=" N THR A 93 " -0.076 2.00e-02 2.50e+03 ... (remaining 3875 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 1945 2.08 - 2.71: 40470 2.71 - 3.34: 77908 3.34 - 3.97: 104516 3.97 - 4.60: 155602 Nonbonded interactions: 380441 Sorted by model distance: nonbonded pdb=" OE1 GLN D 69 " pdb=" H GLN D 69 " model vdw 1.449 2.450 nonbonded pdb=" OE1 GLN A 217 " pdb=" H GLN A 217 " model vdw 1.455 2.450 nonbonded pdb=" OE1 GLU A 420 " pdb=" H GLU A 420 " model vdw 1.486 2.450 nonbonded pdb=" O THR B 50 " pdb="HG23 THR B 50 " model vdw 1.499 2.620 nonbonded pdb=" H ARG A 661 " pdb=" HD2 ARG A 661 " model vdw 1.561 2.270 ... (remaining 380436 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.880 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: 0.420 Extract box with map and model: 0.910 Check model and map are aligned: 0.170 Set scattering table: 0.220 Process input model: 53.310 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.120 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6049 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 : 0.014 0.071 12965 Z= 0.919 Angle : 1.687 11.523 17629 Z= 1.133 Chirality : 0.077 0.343 1929 Planarity : 0.013 0.132 2326 Dihedral : 11.005 88.270 4697 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 3.84 % Allowed : 9.36 % Favored : 86.80 % Rotamer: Outliers : 0.15 % Allowed : 0.59 % Favored : 99.27 % Cbeta Deviations : 0.07 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % 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: -2.52 (0.19), residues: 1614 helix: -0.21 (0.23), residues: 348 sheet: -1.84 (0.24), residues: 404 loop : -2.24 (0.20), residues: 862 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.008 TRP E 73 HIS 0.009 0.002 HIS A 677 PHE 0.058 0.005 PHE A 395 TYR 0.064 0.008 TYR D 205 ARG 0.009 0.001 ARG A 661 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 123 time to evaluate : 1.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 90 THR cc_start: 0.6253 (m) cc_final: 0.5950 (m) REVERT: A 539 MET cc_start: 0.6928 (mpp) cc_final: 0.5961 (mpp) outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.7083 time to fit residues: 123.0753 Evaluate side-chains 87 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 135 optimal weight: 9.9990 chunk 121 optimal weight: 10.0000 chunk 67 optimal weight: 5.9990 chunk 41 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 48 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN B 302 ASN E 52 GLN A 538 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.035665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2862 r_free = 0.2862 target = 0.024582 restraints weight = 502850.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.025784 restraints weight = 293942.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.026637 restraints weight = 196227.559| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.2238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 12965 Z= 0.350 Angle : 0.794 8.340 17629 Z= 0.451 Chirality : 0.046 0.178 1929 Planarity : 0.007 0.126 2326 Dihedral : 6.109 31.329 1781 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 13.11 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.54 % Favored : 89.59 % Rotamer: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.40 (0.20), residues: 1614 helix: 0.01 (0.25), residues: 359 sheet: -1.90 (0.24), residues: 421 loop : -2.16 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 546 HIS 0.010 0.003 HIS E 83 PHE 0.030 0.003 PHE A 395 TYR 0.029 0.002 TYR A 686 ARG 0.007 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.923 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 PHE cc_start: 0.9423 (m-10) cc_final: 0.9220 (m-10) REVERT: B 292 ASP cc_start: 0.8383 (t70) cc_final: 0.8043 (t70) REVERT: A 539 MET cc_start: 0.9402 (mpp) cc_final: 0.9151 (mpp) REVERT: A 717 GLU cc_start: 0.9103 (mt-10) cc_final: 0.8835 (mm-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.6671 time to fit residues: 98.2081 Evaluate side-chains 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 97 optimal weight: 9.9990 chunk 127 optimal weight: 6.9990 chunk 103 optimal weight: 10.0000 chunk 111 optimal weight: 0.0070 chunk 34 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 40 optimal weight: 6.9990 chunk 45 optimal weight: 40.0000 chunk 152 optimal weight: 2.9990 overall best weight: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 324 HIS ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 178 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.034662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.024410 restraints weight = 514961.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.025572 restraints weight = 297412.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.026389 restraints weight = 195424.653| |-----------------------------------------------------------------------------| r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 12965 Z= 0.283 Angle : 0.681 8.174 17629 Z= 0.383 Chirality : 0.043 0.154 1929 Planarity : 0.006 0.128 2326 Dihedral : 5.957 34.683 1781 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.62 % Allowed : 11.83 % Favored : 87.55 % Rotamer: Outliers : 0.07 % Allowed : 0.73 % Favored : 99.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.51 (0.20), residues: 1614 helix: 0.03 (0.25), residues: 367 sheet: -1.97 (0.25), residues: 415 loop : -2.32 (0.20), residues: 832 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 776 HIS 0.006 0.002 HIS A 555 PHE 0.031 0.002 PHE A 395 TYR 0.015 0.002 TYR B 263 ARG 0.012 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 97 time to evaluate : 1.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 42 PHE cc_start: 0.9433 (m-10) cc_final: 0.9212 (m-10) REVERT: B 292 ASP cc_start: 0.8294 (t70) cc_final: 0.8001 (t70) REVERT: D 111 MET cc_start: 0.9704 (mmm) cc_final: 0.9262 (mmm) REVERT: A 142 TYR cc_start: 0.9453 (t80) cc_final: 0.9062 (t80) outliers start: 1 outliers final: 1 residues processed: 98 average time/residue: 0.6568 time to fit residues: 89.6901 Evaluate side-chains 81 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 80 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 143 optimal weight: 6.9990 chunk 70 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 40.0000 chunk 112 optimal weight: 0.0470 chunk 97 optimal weight: 4.9990 chunk 126 optimal weight: 7.9990 chunk 107 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 463 ASN ** A 523 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.034947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.025648 restraints weight = 520081.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.026748 restraints weight = 285321.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.027485 restraints weight = 185618.134| |-----------------------------------------------------------------------------| r_work (final): 0.2904 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 12965 Z= 0.311 Angle : 0.680 6.868 17629 Z= 0.382 Chirality : 0.043 0.159 1929 Planarity : 0.006 0.118 2326 Dihedral : 6.043 33.818 1781 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.62 % Allowed : 12.39 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.72 (0.20), residues: 1614 helix: -0.19 (0.24), residues: 372 sheet: -1.97 (0.25), residues: 404 loop : -2.51 (0.20), residues: 838 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 48 HIS 0.010 0.002 HIS A 625 PHE 0.028 0.002 PHE A 395 TYR 0.019 0.002 TYR A 686 ARG 0.009 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8332 (t70) cc_final: 0.8021 (t70) REVERT: D 111 MET cc_start: 0.9721 (mmm) cc_final: 0.9329 (mmm) REVERT: D 218 MET cc_start: 0.9387 (ttm) cc_final: 0.9161 (ttt) REVERT: A 142 TYR cc_start: 0.9506 (t80) cc_final: 0.9094 (t80) REVERT: A 372 MET cc_start: 0.7256 (ptm) cc_final: 0.6589 (ppp) REVERT: A 389 LEU cc_start: 0.9633 (mm) cc_final: 0.9412 (mm) REVERT: A 717 GLU cc_start: 0.8953 (mp0) cc_final: 0.8563 (mp0) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.6653 time to fit residues: 79.6522 Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 3.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 106 optimal weight: 9.9990 chunk 84 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 152 optimal weight: 5.9990 chunk 144 optimal weight: 9.9990 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 360 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.034133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.024076 restraints weight = 523847.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.025189 restraints weight = 302439.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.025995 restraints weight = 199664.292| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 12965 Z= 0.236 Angle : 0.618 7.030 17629 Z= 0.343 Chirality : 0.042 0.160 1929 Planarity : 0.006 0.113 2326 Dihedral : 5.906 34.307 1781 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.21 % Favored : 87.30 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.57 (0.20), residues: 1614 helix: 0.17 (0.25), residues: 367 sheet: -2.03 (0.25), residues: 411 loop : -2.45 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 635 HIS 0.007 0.002 HIS A 625 PHE 0.024 0.002 PHE A 395 TYR 0.023 0.002 TYR A 266 ARG 0.006 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 2.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8408 (t70) cc_final: 0.8113 (t70) REVERT: D 111 MET cc_start: 0.9708 (mmm) cc_final: 0.9311 (mmm) REVERT: D 218 MET cc_start: 0.9379 (ttm) cc_final: 0.9107 (ttt) REVERT: A 142 TYR cc_start: 0.9434 (t80) cc_final: 0.9053 (t80) REVERT: A 372 MET cc_start: 0.7638 (ptm) cc_final: 0.6974 (ppp) REVERT: A 389 LEU cc_start: 0.9646 (mm) cc_final: 0.9435 (mm) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.6889 time to fit residues: 84.6487 Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 42 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 56 optimal weight: 10.0000 chunk 107 optimal weight: 0.0270 chunk 136 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 159 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 overall best weight: 6.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 186 HIS ** A 538 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 = 0.3133 r_free = 0.3133 target = 0.033185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.023549 restraints weight = 558409.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.024624 restraints weight = 318213.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.025369 restraints weight = 209776.959| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8117 moved from start: 0.4407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 12965 Z= 0.348 Angle : 0.693 6.776 17629 Z= 0.392 Chirality : 0.043 0.162 1929 Planarity : 0.006 0.107 2326 Dihedral : 6.195 34.575 1781 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 19.12 Ramachandran Plot: Outliers : 0.56 % Allowed : 14.00 % Favored : 85.44 % Rotamer: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.96 (0.20), residues: 1614 helix: -0.22 (0.25), residues: 364 sheet: -2.21 (0.24), residues: 415 loop : -2.68 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 635 HIS 0.007 0.002 HIS A 625 PHE 0.025 0.002 PHE A 395 TYR 0.017 0.002 TYR A 296 ARG 0.010 0.001 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.915 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8440 (t70) cc_final: 0.8195 (t70) REVERT: A 372 MET cc_start: 0.7330 (ptm) cc_final: 0.6524 (ppp) REVERT: A 389 LEU cc_start: 0.9607 (mm) cc_final: 0.9396 (mm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6719 time to fit residues: 74.2836 Evaluate side-chains 73 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 1.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 58 optimal weight: 9.9990 chunk 81 optimal weight: 2.9990 chunk 53 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 chunk 8 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 10 optimal weight: 0.9990 chunk 153 optimal weight: 3.9990 chunk 84 optimal weight: 0.9980 chunk 155 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN A 244 GLN ** A 538 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 = 0.3371 r_free = 0.3371 target = 0.042123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.032586 restraints weight = 708513.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.033685 restraints weight = 382014.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.034673 restraints weight = 247524.556| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12965 Z= 0.165 Angle : 0.574 6.859 17629 Z= 0.315 Chirality : 0.043 0.166 1929 Planarity : 0.005 0.107 2326 Dihedral : 5.758 33.039 1781 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.09 % Favored : 88.35 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.48 (0.20), residues: 1614 helix: 0.49 (0.26), residues: 367 sheet: -2.05 (0.24), residues: 410 loop : -2.47 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 PHE 0.018 0.001 PHE A 395 TYR 0.022 0.002 TYR A 266 ARG 0.004 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 2.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8399 (t70) cc_final: 0.8099 (t70) REVERT: D 218 MET cc_start: 0.9224 (ttt) cc_final: 0.8512 (tpp) REVERT: A 142 TYR cc_start: 0.9512 (t80) cc_final: 0.9120 (t80) REVERT: A 372 MET cc_start: 0.7502 (ptm) cc_final: 0.6855 (ppp) REVERT: A 389 LEU cc_start: 0.9629 (mm) cc_final: 0.9385 (mm) REVERT: A 717 GLU cc_start: 0.8851 (mp0) cc_final: 0.8466 (mp0) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.6541 time to fit residues: 80.0832 Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 2.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 70 optimal weight: 10.0000 chunk 116 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 142 optimal weight: 9.9990 chunk 69 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 109 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 135 optimal weight: 10.0000 chunk 150 optimal weight: 20.0000 chunk 4 optimal weight: 2.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 168 GLN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 753 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.033624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.023651 restraints weight = 538069.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.024759 restraints weight = 308196.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.025536 restraints weight = 202717.115| |-----------------------------------------------------------------------------| r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12965 Z= 0.236 Angle : 0.595 6.632 17629 Z= 0.331 Chirality : 0.042 0.176 1929 Planarity : 0.005 0.109 2326 Dihedral : 5.767 32.805 1781 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.01 % Favored : 86.43 % Rotamer: Outliers : 0.00 % Allowed : 0.59 % Favored : 99.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.58 (0.20), residues: 1614 helix: 0.44 (0.26), residues: 367 sheet: -2.14 (0.24), residues: 400 loop : -2.54 (0.20), residues: 847 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.005 0.002 HIS A 625 PHE 0.020 0.002 PHE A 395 TYR 0.015 0.002 TYR B 263 ARG 0.008 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 79 time to evaluate : 1.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8474 (t70) cc_final: 0.8220 (t70) REVERT: D 111 MET cc_start: 0.9727 (mmm) cc_final: 0.9323 (mmm) REVERT: A 142 TYR cc_start: 0.9480 (t80) cc_final: 0.9109 (t80) REVERT: A 372 MET cc_start: 0.7564 (ptm) cc_final: 0.6898 (ppp) REVERT: A 389 LEU cc_start: 0.9620 (mm) cc_final: 0.9392 (mm) outliers start: 0 outliers final: 0 residues processed: 79 average time/residue: 0.6523 time to fit residues: 73.8287 Evaluate side-chains 77 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 2.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 55 optimal weight: 7.9990 chunk 125 optimal weight: 0.9990 chunk 115 optimal weight: 10.0000 chunk 132 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 60 optimal weight: 0.9980 chunk 52 optimal weight: 40.0000 chunk 94 optimal weight: 9.9990 chunk 2 optimal weight: 0.5980 chunk 90 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.033942 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.023921 restraints weight = 537183.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.025019 restraints weight = 306707.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.025796 restraints weight = 202501.502| |-----------------------------------------------------------------------------| r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12965 Z= 0.191 Angle : 0.569 6.670 17629 Z= 0.314 Chirality : 0.042 0.173 1929 Planarity : 0.005 0.110 2326 Dihedral : 5.673 32.438 1781 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.14 % Favored : 87.36 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.47 (0.20), residues: 1614 helix: 0.66 (0.26), residues: 367 sheet: -2.11 (0.24), residues: 401 loop : -2.50 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 PHE 0.034 0.002 PHE A 804 TYR 0.015 0.002 TYR A 266 ARG 0.006 0.000 ARG A 734 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8468 (t70) cc_final: 0.8204 (t70) REVERT: D 218 MET cc_start: 0.9280 (ttt) cc_final: 0.8676 (tpp) REVERT: A 142 TYR cc_start: 0.9490 (t80) cc_final: 0.9130 (t80) REVERT: A 372 MET cc_start: 0.7486 (ptm) cc_final: 0.6872 (ppp) REVERT: A 389 LEU cc_start: 0.9618 (mm) cc_final: 0.9378 (mm) REVERT: A 717 GLU cc_start: 0.8939 (mp0) cc_final: 0.8591 (mp0) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.6515 time to fit residues: 75.8432 Evaluate side-chains 77 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 2 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 3 optimal weight: 9.9990 chunk 139 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 105 optimal weight: 10.0000 chunk 80 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 66 optimal weight: 0.7980 chunk 138 optimal weight: 6.9990 overall best weight: 5.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 30 HIS ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.033163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.023469 restraints weight = 548019.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.024522 restraints weight = 316329.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.025243 restraints weight = 210691.218| |-----------------------------------------------------------------------------| r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 12965 Z= 0.289 Angle : 0.632 6.322 17629 Z= 0.354 Chirality : 0.042 0.174 1929 Planarity : 0.005 0.110 2326 Dihedral : 5.835 32.464 1781 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.75 % Favored : 85.75 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % 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: -2.72 (0.20), residues: 1614 helix: 0.39 (0.26), residues: 366 sheet: -2.22 (0.24), residues: 402 loop : -2.65 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 635 HIS 0.007 0.002 HIS A 625 PHE 0.020 0.002 PHE A 395 TYR 0.014 0.002 TYR B 263 ARG 0.009 0.001 ARG A 734 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3228 Ramachandran restraints generated. 1614 Oldfield, 0 Emsley, 1614 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 292 ASP cc_start: 0.8548 (t70) cc_final: 0.8270 (t70) REVERT: D 111 MET cc_start: 0.9721 (mmm) cc_final: 0.9343 (mmm) REVERT: A 372 MET cc_start: 0.7669 (ptm) cc_final: 0.7042 (ppp) REVERT: A 389 LEU cc_start: 0.9636 (mm) cc_final: 0.9432 (mm) outliers start: 0 outliers final: 0 residues processed: 78 average time/residue: 0.6535 time to fit residues: 71.8951 Evaluate side-chains 77 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 77 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 145 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 127 optimal weight: 0.3980 chunk 75 optimal weight: 7.9990 chunk 0 optimal weight: 20.0000 chunk 91 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 chunk 159 optimal weight: 10.0000 chunk 37 optimal weight: 10.0000 overall best weight: 5.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 302 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.033189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.023496 restraints weight = 545304.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.024554 restraints weight = 314306.142| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.025278 restraints weight = 209510.637| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.5116 Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: