Starting phenix.real_space_refine on Fri Sep 19 09:22:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5ljo_4061/09_2025/5ljo_4061.cif Found real_map, /net/cci-nas-00/data/ceres_data/5ljo_4061/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/5ljo_4061/09_2025/5ljo_4061.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5ljo_4061/09_2025/5ljo_4061.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5ljo_4061/09_2025/5ljo_4061.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5ljo_4061/09_2025/5ljo_4061.map" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.53, per 1000 atoms: 0.18 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: 2.20 Conformation dependent library (CDL) restraints added in 823.7 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.70 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: 6.63 Time building geometry restraints manager: 3.08 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 25.190 Find NCS groups from input model: 0.090 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: 0.020 Load rotamer database and sin/cos tables:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.610 ------------------------------------------------------------------------------- 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= 0.887 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.009 0.001 ARG A 661 TYR 0.064 0.008 TYR D 205 PHE 0.058 0.005 PHE A 395 TRP 0.041 0.008 TRP E 73 HIS 0.009 0.002 HIS A 677 Details of bonding type rmsd covalent geometry : bond 0.01414 (12965) covalent geometry : angle 1.68690 (17629) hydrogen bonds : bond 0.15200 ( 563) hydrogen bonds : angle 10.18864 ( 1542) *********************** 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 : 0.725 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: symmetry clash REVERT: E 90 THR cc_start: 0.6253 (m) cc_final: 0.5935 (m) REVERT: A 539 MET cc_start: 0.6928 (mpp) cc_final: 0.5971 (mpp) outliers start: 2 outliers final: 1 residues processed: 125 average time/residue: 0.3204 time to fit residues: 55.0232 Evaluate side-chains 88 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 87 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 98 optimal weight: 5.9990 chunk 107 optimal weight: 7.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 5.9990 chunk 149 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 = 0.3221 r_free = 0.3221 target = 0.035467 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.024624 restraints weight = 503218.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.025829 restraints weight = 295062.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.026685 restraints weight = 195545.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.027273 restraints weight = 143262.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.027667 restraints weight = 113860.975| |-----------------------------------------------------------------------------| r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 12965 Z= 0.279 Angle : 0.791 8.172 17629 Z= 0.448 Chirality : 0.045 0.176 1929 Planarity : 0.007 0.126 2326 Dihedral : 6.155 32.105 1781 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.87 % Allowed : 9.60 % Favored : 89.53 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.20), residues: 1614 helix: -0.00 (0.25), residues: 360 sheet: -1.94 (0.24), residues: 430 loop : -2.18 (0.21), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 734 TYR 0.030 0.003 TYR A 686 PHE 0.031 0.003 PHE A 395 TRP 0.014 0.002 TRP A 546 HIS 0.010 0.003 HIS E 83 Details of bonding type rmsd covalent geometry : bond 0.00526 (12965) covalent geometry : angle 0.79125 (17629) hydrogen bonds : bond 0.06165 ( 563) hydrogen bonds : angle 8.66652 ( 1542) *********************** 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 : 0.733 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: 0.9427 (m-10) cc_final: 0.9186 (m-10) REVERT: B 292 ASP cc_start: 0.8348 (t70) cc_final: 0.8014 (t70) REVERT: A 539 MET cc_start: 0.9411 (mpp) cc_final: 0.9152 (mpp) REVERT: A 717 GLU cc_start: 0.9077 (mt-10) cc_final: 0.8798 (mm-30) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.3307 time to fit residues: 47.7941 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 : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 146 optimal weight: 7.9990 chunk 118 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 11 optimal weight: 7.9990 chunk 122 optimal weight: 0.6980 chunk 27 optimal weight: 6.9990 chunk 145 optimal weight: 6.9990 chunk 126 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 149 optimal weight: 7.9990 overall best weight: 5.7388 ------------------------------------------------------------------------------- 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 A 523 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.035016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.024351 restraints weight = 503298.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.025519 restraints weight = 294150.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.026360 restraints weight = 195823.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.026939 restraints weight = 143996.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.027329 restraints weight = 114737.338| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8061 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 12965 Z= 0.263 Angle : 0.712 8.350 17629 Z= 0.402 Chirality : 0.043 0.155 1929 Planarity : 0.006 0.129 2326 Dihedral : 6.091 34.588 1781 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.95 Ramachandran Plot: Outliers : 0.68 % Allowed : 11.59 % Favored : 87.73 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.20), residues: 1614 helix: -0.09 (0.25), residues: 365 sheet: -1.94 (0.25), residues: 420 loop : -2.34 (0.20), residues: 829 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 734 TYR 0.017 0.002 TYR A 348 PHE 0.029 0.002 PHE A 395 TRP 0.013 0.002 TRP A 635 HIS 0.006 0.002 HIS A 555 Details of bonding type rmsd covalent geometry : bond 0.00497 (12965) covalent geometry : angle 0.71229 (17629) hydrogen bonds : bond 0.05457 ( 563) hydrogen bonds : angle 8.37853 ( 1542) *********************** 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 92 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 0.850 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: B 42 PHE cc_start: 0.9436 (m-10) cc_final: 0.9211 (m-10) REVERT: B 292 ASP cc_start: 0.8312 (t70) cc_final: 0.7984 (t70) REVERT: D 218 MET cc_start: 0.9332 (ttm) cc_final: 0.9061 (ttt) REVERT: A 142 TYR cc_start: 0.9426 (t80) cc_final: 0.9040 (t80) REVERT: A 717 GLU cc_start: 0.9152 (mt-10) cc_final: 0.8920 (mp0) outliers start: 0 outliers final: 0 residues processed: 92 average time/residue: 0.3148 time to fit residues: 40.3628 Evaluate side-chains 80 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 92 optimal weight: 9.9990 chunk 114 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 153 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 124 optimal weight: 6.9990 chunk 86 optimal weight: 5.9990 chunk 63 optimal weight: 9.9990 chunk 45 optimal weight: 20.0000 chunk 64 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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** B 360 GLN A 30 HIS A 463 ASN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 625 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.033779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.024852 restraints weight = 523564.985| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.025853 restraints weight = 303487.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.026561 restraints weight = 200972.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.027019 restraints weight = 147839.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.027317 restraints weight = 118888.482| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 12965 Z= 0.306 Angle : 0.757 7.453 17629 Z= 0.429 Chirality : 0.044 0.166 1929 Planarity : 0.007 0.119 2326 Dihedral : 6.332 33.880 1781 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 19.77 Ramachandran Plot: Outliers : 0.56 % Allowed : 13.38 % Favored : 86.06 % Rotamer: Outliers : 0.22 % Allowed : 2.06 % Favored : 97.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.05 (0.19), residues: 1614 helix: -0.54 (0.24), residues: 365 sheet: -2.19 (0.25), residues: 412 loop : -2.66 (0.20), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.030 0.001 ARG C 134 TYR 0.020 0.003 TYR A 296 PHE 0.034 0.003 PHE A 395 TRP 0.018 0.002 TRP A 635 HIS 0.015 0.003 HIS A 625 Details of bonding type rmsd covalent geometry : bond 0.00588 (12965) covalent geometry : angle 0.75709 (17629) hydrogen bonds : bond 0.05356 ( 563) hydrogen bonds : angle 8.29004 ( 1542) *********************** 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 83 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.513 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: 0.8300 (t70) cc_final: 0.7964 (t70) REVERT: D 111 MET cc_start: 0.9690 (mmm) cc_final: 0.9328 (mmm) REVERT: D 218 MET cc_start: 0.9379 (ttm) cc_final: 0.9156 (ttt) REVERT: A 142 TYR cc_start: 0.9419 (t80) cc_final: 0.9037 (t80) REVERT: A 717 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8892 (mp0) outliers start: 3 outliers final: 2 residues processed: 83 average time/residue: 0.3284 time to fit residues: 37.9024 Evaluate side-chains 77 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 75 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 123 optimal weight: 20.0000 chunk 1 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 0.0470 chunk 111 optimal weight: 6.9990 chunk 42 optimal weight: 9.9990 chunk 94 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 154 optimal weight: 10.0000 overall best weight: 4.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 276 GLN ** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3162 r_free = 0.3162 target = 0.034003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.024007 restraints weight = 524105.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.025128 restraints weight = 298381.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.025895 restraints weight = 196878.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.026416 restraints weight = 144442.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.026760 restraints weight = 115534.302| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 12965 Z= 0.201 Angle : 0.638 7.033 17629 Z= 0.355 Chirality : 0.043 0.159 1929 Planarity : 0.006 0.113 2326 Dihedral : 6.130 34.550 1781 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 11.63 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.52 % Favored : 86.99 % Rotamer: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.83 (0.20), residues: 1614 helix: -0.12 (0.25), residues: 367 sheet: -2.24 (0.24), residues: 411 loop : -2.53 (0.20), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 734 TYR 0.032 0.002 TYR A 266 PHE 0.023 0.002 PHE A 395 TRP 0.012 0.001 TRP A 635 HIS 0.005 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00376 (12965) covalent geometry : angle 0.63758 (17629) hydrogen bonds : bond 0.04629 ( 563) hydrogen bonds : angle 7.89780 ( 1542) *********************** 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 84 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.689 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: 0.8358 (t70) cc_final: 0.8027 (t70) REVERT: D 111 MET cc_start: 0.9708 (mmm) cc_final: 0.9311 (mmm) REVERT: D 218 MET cc_start: 0.9386 (ttm) cc_final: 0.9129 (ttt) REVERT: A 142 TYR cc_start: 0.9423 (t80) cc_final: 0.9030 (t80) REVERT: A 372 MET cc_start: 0.7490 (ptm) cc_final: 0.6745 (ppp) REVERT: A 389 LEU cc_start: 0.9645 (mm) cc_final: 0.9438 (mm) REVERT: A 717 GLU cc_start: 0.9122 (mt-10) cc_final: 0.8868 (mp0) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.3030 time to fit residues: 35.6847 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 : 0.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 131 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 20 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 77 optimal weight: 8.9990 chunk 53 optimal weight: 0.0980 chunk 150 optimal weight: 20.0000 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 54 optimal weight: 5.9990 overall best weight: 4.2186 ------------------------------------------------------------------------------- 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 A 186 HIS A 244 GLN ** A 538 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.034906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.025499 restraints weight = 514489.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.026596 restraints weight = 287059.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.027330 restraints weight = 187475.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.027814 restraints weight = 137272.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.028123 restraints weight = 110124.043| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.4267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 12965 Z= 0.203 Angle : 0.620 6.978 17629 Z= 0.346 Chirality : 0.043 0.179 1929 Planarity : 0.005 0.109 2326 Dihedral : 6.008 33.892 1781 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.64 % Favored : 86.80 % Rotamer: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.82 (0.20), residues: 1614 helix: 0.06 (0.25), residues: 367 sheet: -2.30 (0.24), residues: 422 loop : -2.57 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 734 TYR 0.017 0.002 TYR B 263 PHE 0.023 0.002 PHE A 395 TRP 0.011 0.001 TRP A 635 HIS 0.006 0.002 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00388 (12965) covalent geometry : angle 0.62029 (17629) hydrogen bonds : bond 0.04411 ( 563) hydrogen bonds : angle 7.68050 ( 1542) *********************** 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 80 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.627 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: A 142 TYR cc_start: 0.9566 (t80) cc_final: 0.9157 (t80) REVERT: A 372 MET cc_start: 0.7084 (ptm) cc_final: 0.6351 (ppp) REVERT: A 389 LEU cc_start: 0.9600 (mm) cc_final: 0.9350 (mm) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3128 time to fit residues: 35.4842 Evaluate side-chains 75 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 20 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 107 optimal weight: 0.0040 chunk 45 optimal weight: 40.0000 chunk 67 optimal weight: 6.9990 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 53 optimal weight: 0.0040 overall best weight: 2.3608 ------------------------------------------------------------------------------- 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 = 0.3177 r_free = 0.3177 target = 0.034361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.023973 restraints weight = 527037.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.025125 restraints weight = 304757.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.025929 restraints weight = 199666.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.026485 restraints weight = 146175.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.026843 restraints weight = 116707.854| |-----------------------------------------------------------------------------| r_work (final): 0.2918 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 12965 Z= 0.137 Angle : 0.574 6.953 17629 Z= 0.315 Chirality : 0.043 0.169 1929 Planarity : 0.005 0.109 2326 Dihedral : 5.773 33.193 1781 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.56 % Allowed : 11.52 % Favored : 87.92 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.56 (0.20), residues: 1614 helix: 0.46 (0.26), residues: 367 sheet: -2.21 (0.24), residues: 419 loop : -2.46 (0.20), residues: 828 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.016 0.001 TYR B 263 PHE 0.019 0.001 PHE A 395 TRP 0.009 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00262 (12965) covalent geometry : angle 0.57372 (17629) hydrogen bonds : bond 0.03983 ( 563) hydrogen bonds : angle 7.32079 ( 1542) *********************** 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 85 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.759 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: 0.8412 (t70) cc_final: 0.8126 (t70) REVERT: A 142 TYR cc_start: 0.9506 (t80) cc_final: 0.9111 (t80) REVERT: A 367 ARG cc_start: 0.9496 (ptp-110) cc_final: 0.9225 (ptt180) REVERT: A 372 MET cc_start: 0.7339 (ptm) cc_final: 0.6682 (ppp) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.3193 time to fit residues: 37.9651 Evaluate side-chains 75 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 132 optimal weight: 8.9990 chunk 147 optimal weight: 6.9990 chunk 98 optimal weight: 10.0000 chunk 139 optimal weight: 8.9990 chunk 135 optimal weight: 0.9990 chunk 68 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 143 optimal weight: 0.9990 chunk 49 optimal weight: 20.0000 chunk 141 optimal weight: 4.9990 chunk 128 optimal weight: 5.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 D 99 ASN ** 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 = 0.3165 r_free = 0.3165 target = 0.034338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.023834 restraints weight = 515036.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.024941 restraints weight = 302103.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.025726 restraints weight = 202143.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.026258 restraints weight = 150020.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.026635 restraints weight = 120981.030| |-----------------------------------------------------------------------------| r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.4564 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= 0.186 Angle : 0.593 6.756 17629 Z= 0.330 Chirality : 0.042 0.178 1929 Planarity : 0.005 0.111 2326 Dihedral : 5.786 32.679 1781 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.56 % Allowed : 12.70 % Favored : 86.74 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.63 (0.20), residues: 1614 helix: 0.44 (0.26), residues: 367 sheet: -2.28 (0.24), residues: 412 loop : -2.52 (0.20), residues: 835 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 734 TYR 0.026 0.002 TYR A 266 PHE 0.020 0.002 PHE A 395 TRP 0.010 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00356 (12965) covalent geometry : angle 0.59341 (17629) hydrogen bonds : bond 0.04150 ( 563) hydrogen bonds : angle 7.33877 ( 1542) *********************** 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 80 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.669 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: B 292 ASP cc_start: 0.8479 (t70) cc_final: 0.8192 (t70) REVERT: D 218 MET cc_start: 0.9410 (ttm) cc_final: 0.9188 (ttt) REVERT: A 142 TYR cc_start: 0.9452 (t80) cc_final: 0.9077 (t80) REVERT: A 372 MET cc_start: 0.7529 (ptm) cc_final: 0.6863 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3267 time to fit residues: 36.3461 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 : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 68 optimal weight: 8.9990 chunk 24 optimal weight: 9.9990 chunk 136 optimal weight: 3.9990 chunk 90 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 122 optimal weight: 0.8980 chunk 109 optimal weight: 7.9990 chunk 123 optimal weight: 7.9990 chunk 56 optimal weight: 0.9990 chunk 17 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** ** 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 = 0.3341 r_free = 0.3341 target = 0.041230 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.031605 restraints weight = 718471.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.032663 restraints weight = 393051.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.033631 restraints weight = 255118.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.034225 restraints weight = 187912.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.034432 restraints weight = 151930.878| |-----------------------------------------------------------------------------| r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.4701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12965 Z= 0.183 Angle : 0.590 6.639 17629 Z= 0.328 Chirality : 0.042 0.173 1929 Planarity : 0.005 0.110 2326 Dihedral : 5.785 32.505 1781 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.50 % Allowed : 12.95 % Favored : 86.56 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.65 (0.20), residues: 1614 helix: 0.47 (0.26), residues: 369 sheet: -2.32 (0.23), residues: 422 loop : -2.53 (0.20), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 734 TYR 0.021 0.002 TYR A 266 PHE 0.039 0.002 PHE A 804 TRP 0.011 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00347 (12965) covalent geometry : angle 0.58955 (17629) hydrogen bonds : bond 0.04094 ( 563) hydrogen bonds : angle 7.31157 ( 1542) *********************** 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 80 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 0.758 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: 0.8455 (t70) cc_final: 0.8144 (t70) REVERT: D 111 MET cc_start: 0.9736 (mmm) cc_final: 0.9383 (mmm) REVERT: D 218 MET cc_start: 0.9406 (ttm) cc_final: 0.9187 (ttt) REVERT: A 142 TYR cc_start: 0.9532 (t80) cc_final: 0.9145 (t80) REVERT: A 367 ARG cc_start: 0.9433 (ptp-110) cc_final: 0.9177 (ptp90) REVERT: A 372 MET cc_start: 0.7545 (ptm) cc_final: 0.6924 (ppp) outliers start: 0 outliers final: 0 residues processed: 80 average time/residue: 0.3382 time to fit residues: 37.8803 Evaluate side-chains 76 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 13 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 2 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 91 optimal weight: 0.0070 chunk 25 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 154 optimal weight: 9.9990 chunk 70 optimal weight: 5.9990 chunk 106 optimal weight: 4.9990 overall best weight: 2.8004 ------------------------------------------------------------------------------- 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 = 0.3358 r_free = 0.3358 target = 0.041696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.032128 restraints weight = 709674.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 61)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.033154 restraints weight = 386080.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 70)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.034152 restraints weight = 249828.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.034756 restraints weight = 182028.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 64)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.035131 restraints weight = 147297.706| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 12965 Z= 0.141 Angle : 0.555 6.510 17629 Z= 0.305 Chirality : 0.042 0.175 1929 Planarity : 0.005 0.110 2326 Dihedral : 5.606 31.623 1781 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.50 % Allowed : 11.96 % Favored : 87.55 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.48 (0.20), residues: 1614 helix: 0.76 (0.26), residues: 368 sheet: -2.31 (0.23), residues: 423 loop : -2.45 (0.21), residues: 823 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 734 TYR 0.017 0.001 TYR A 266 PHE 0.017 0.001 PHE A 395 TRP 0.010 0.001 TRP A 776 HIS 0.005 0.001 HIS B 347 Details of bonding type rmsd covalent geometry : bond 0.00269 (12965) covalent geometry : angle 0.55468 (17629) hydrogen bonds : bond 0.03783 ( 563) hydrogen bonds : angle 7.06603 ( 1542) ********************** 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 83 residues out of total 1362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.746 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 42 PHE cc_start: 0.9471 (m-80) cc_final: 0.9260 (m-10) REVERT: B 292 ASP cc_start: 0.8429 (t70) cc_final: 0.8106 (t70) REVERT: D 111 MET cc_start: 0.9749 (mmm) cc_final: 0.9364 (mmm) REVERT: D 218 MET cc_start: 0.9448 (ttm) cc_final: 0.9171 (ttt) REVERT: A 142 TYR cc_start: 0.9548 (t80) cc_final: 0.9174 (t80) REVERT: A 372 MET cc_start: 0.7498 (ptm) cc_final: 0.6822 (ppp) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.3217 time to fit residues: 37.5459 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 : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 160 random chunks: chunk 140 optimal weight: 8.9990 chunk 156 optimal weight: 10.0000 chunk 54 optimal weight: 9.9990 chunk 74 optimal weight: 0.0980 chunk 47 optimal weight: 4.9990 chunk 56 optimal weight: 8.9990 chunk 107 optimal weight: 0.0030 chunk 15 optimal weight: 20.0000 chunk 63 optimal weight: 9.9990 chunk 124 optimal weight: 9.9990 chunk 50 optimal weight: 20.0000 overall best weight: 4.6196 ------------------------------------------------------------------------------- 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** ** 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 = 0.3320 r_free = 0.3320 target = 0.040538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.031122 restraints weight = 724990.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.032142 restraints weight = 401478.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.033024 restraints weight = 260993.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.033510 restraints weight = 192038.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 56)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.033988 restraints weight = 159455.312| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.5045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12965 Z= 0.203 Angle : 0.604 6.235 17629 Z= 0.337 Chirality : 0.042 0.174 1929 Planarity : 0.005 0.110 2326 Dihedral : 5.771 32.123 1781 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.75 Ramachandran Plot: Outliers : 0.50 % Allowed : 13.26 % Favored : 86.25 % Rotamer: Outliers : 0.00 % Allowed : 0.07 % Favored : 99.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.70 (0.20), residues: 1614 helix: 0.49 (0.26), residues: 373 sheet: -2.33 (0.23), residues: 419 loop : -2.63 (0.20), residues: 822 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 734 TYR 0.015 0.002 TYR A 255 PHE 0.023 0.002 PHE A 718 TRP 0.014 0.002 TRP A 635 HIS 0.005 0.002 HIS A 186 Details of bonding type rmsd covalent geometry : bond 0.00391 (12965) covalent geometry : angle 0.60404 (17629) hydrogen bonds : bond 0.04065 ( 563) hydrogen bonds : angle 7.24329 ( 1542) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4443.42 seconds wall clock time: 76 minutes 50.09 seconds (4610.09 seconds total)