Starting phenix.real_space_refine on Sun May 11 14:12:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.map" model { file = "/net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv1_60917/05_2025/9iv1_60917.cif" } resolution = 2.98 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= 0.002 sd= 0.033 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: 4 Type Number sf(0) Gaussians S 50 5.16 5 C 5293 2.51 5 N 1405 2.21 5 O 1536 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8284 Number of models: 1 Model: "" Number of chains: 6 Chain: "S" Number of atoms: 1698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1698 Classifications: {'peptide': 231} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 49 Chain: "B" Number of atoms: 2496 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2496 Classifications: {'peptide': 338} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 23} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 125 Unresolved non-hydrogen dihedrals: 85 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 5, 'ARG:plan': 9, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 85 Chain: "G" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 401 Classifications: {'peptide': 58} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 4, 'TRANS': 53} Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 38 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 21 Chain: "R" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 255, 1899 Classifications: {'peptide': 255} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 249} Chain breaks: 1 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 93 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1, 'ASP:plan': 1, 'PHE:plan': 3, 'GLU:plan': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "A" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 1769 Classifications: {'peptide': 227} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 6, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 110 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 89 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 8, 'ASN:plan1': 1, 'ARG:plan': 3, 'ASP:plan': 6} Unresolved non-hydrogen planarities: 75 Chain: "R" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 21 Unusual residues: {'DHT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.44, per 1000 atoms: 0.66 Number of scatterers: 8284 At special positions: 0 Unit cell: (97.58, 115.62, 114.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 50 16.00 O 1536 8.00 N 1405 7.00 C 5293 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=1.72 Simple disulfide: pdb=" SG CYS R 632 " - pdb=" SG CYS R 704 " distance=2.02 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: 2.36 Conformation dependent library (CDL) restraints added in 1.1 seconds 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2072 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 12 sheets defined 31.7% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'B' and resid 4 through 26 removed outlier: 4.039A pdb=" N GLU B 10 " --> pdb=" O GLN B 6 " (cutoff:3.500A) removed outlier: 4.870A pdb=" N ALA B 11 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N GLU B 12 " --> pdb=" O ARG B 8 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLN B 13 " --> pdb=" O GLN B 9 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 6 through 24 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'R' and resid 567 through 591 removed outlier: 3.709A pdb=" N GLY R 573 " --> pdb=" O ILE R 569 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N CYS R 574 " --> pdb=" O SER R 570 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N VAL R 578 " --> pdb=" O CYS R 574 " (cutoff:3.500A) Processing helix chain 'R' and resid 600 through 622 removed outlier: 4.899A pdb=" N ALA R 606 " --> pdb=" O TYR R 602 " (cutoff:3.500A) Processing helix chain 'R' and resid 629 through 659 removed outlier: 3.679A pdb=" N PHE R 642 " --> pdb=" O LEU R 638 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N ALA R 646 " --> pdb=" O PHE R 642 " (cutoff:3.500A) Processing helix chain 'R' and resid 671 through 680 Processing helix chain 'R' and resid 681 through 692 Processing helix chain 'R' and resid 720 through 741 removed outlier: 3.755A pdb=" N ILE R 724 " --> pdb=" O ALA R 720 " (cutoff:3.500A) Processing helix chain 'R' and resid 755 through 770 Proline residue: R 767 - end of helix Processing helix chain 'R' and resid 772 through 777 removed outlier: 3.723A pdb=" N PHE R 775 " --> pdb=" O SER R 772 " (cutoff:3.500A) Processing helix chain 'R' and resid 789 through 794 removed outlier: 3.816A pdb=" N LEU R 794 " --> pdb=" O MET R 790 " (cutoff:3.500A) Processing helix chain 'R' and resid 797 through 807 Processing helix chain 'R' and resid 810 through 827 Processing helix chain 'A' and resid 13 through 38 removed outlier: 3.697A pdb=" N GLU A 21 " --> pdb=" O LYS A 17 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG A 22 " --> pdb=" O ALA A 18 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 58 Processing helix chain 'A' and resid 234 through 238 removed outlier: 3.628A pdb=" N CYS A 237 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 278 Processing helix chain 'A' and resid 295 through 303 removed outlier: 3.577A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.012A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 350 removed outlier: 4.367A pdb=" N TYR A 339 " --> pdb=" O THR A 335 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N PHE A 340 " --> pdb=" O ARG A 336 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N PHE A 345 " --> pdb=" O ILE A 341 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 391 removed outlier: 3.745A pdb=" N ILE A 375 " --> pdb=" O ASN A 371 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 391 " --> pdb=" O HIS A 387 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'S' and resid 18 through 21 removed outlier: 3.712A pdb=" N LEU S 20 " --> pdb=" O LEU S 81 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'S' and resid 58 through 60 removed outlier: 3.695A pdb=" N TYR S 50 " --> pdb=" O TYR S 59 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N VAL S 97 " --> pdb=" O HIS S 35 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'S' and resid 128 through 129 removed outlier: 4.006A pdb=" N VAL S 143 " --> pdb=" O ILE S 204 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.702A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.496A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.735A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.865A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 4.862A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.161A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.097A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.822A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 4.258A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.019A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 189 through 192 removed outlier: 4.053A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.764A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 276 through 278 removed outlier: 5.752A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 207 through 214 removed outlier: 3.622A pdb=" N PHE A 212 " --> pdb=" O PHE A 219 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N VAL A 224 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ILE A 244 " --> pdb=" O ILE A 288 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N PHE A 290 " --> pdb=" O ILE A 244 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N PHE A 246 " --> pdb=" O PHE A 290 " (cutoff:3.500A) 359 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 2.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1531 1.33 - 1.45: 2268 1.45 - 1.57: 4598 1.57 - 1.69: 0 1.69 - 1.81: 70 Bond restraints: 8467 Sorted by residual: bond pdb=" CA ALA R 720 " pdb=" C ALA R 720 " ideal model delta sigma weight residual 1.522 1.435 0.086 1.25e-02 6.40e+03 4.77e+01 bond pdb=" CA ALA R 761 " pdb=" C ALA R 761 " ideal model delta sigma weight residual 1.524 1.441 0.083 1.24e-02 6.50e+03 4.51e+01 bond pdb=" CA TRP R 714 " pdb=" C TRP R 714 " ideal model delta sigma weight residual 1.530 1.460 0.070 1.14e-02 7.69e+03 3.79e+01 bond pdb=" CA LEU S 221 " pdb=" C LEU S 221 " ideal model delta sigma weight residual 1.524 1.451 0.072 1.23e-02 6.61e+03 3.47e+01 bond pdb=" CA SER R 742 " pdb=" C SER R 742 " ideal model delta sigma weight residual 1.525 1.461 0.064 1.11e-02 8.12e+03 3.28e+01 ... (remaining 8462 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.99: 11363 2.99 - 5.97: 148 5.97 - 8.96: 27 8.96 - 11.95: 9 11.95 - 14.94: 2 Bond angle restraints: 11549 Sorted by residual: angle pdb=" N PHE R 716 " pdb=" CA PHE R 716 " pdb=" C PHE R 716 " ideal model delta sigma weight residual 114.39 99.45 14.94 1.45e+00 4.76e-01 1.06e+02 angle pdb=" C TYR S 223 " pdb=" N PRO S 224 " pdb=" CA PRO S 224 " ideal model delta sigma weight residual 119.56 111.22 8.34 1.02e+00 9.61e-01 6.69e+01 angle pdb=" N MET R 635 " pdb=" CA MET R 635 " pdb=" C MET R 635 " ideal model delta sigma weight residual 112.87 103.07 9.80 1.20e+00 6.94e-01 6.67e+01 angle pdb=" N PHE R 755 " pdb=" CA PHE R 755 " pdb=" C PHE R 755 " ideal model delta sigma weight residual 113.01 104.30 8.71 1.20e+00 6.94e-01 5.27e+01 angle pdb=" N LEU S 221 " pdb=" CA LEU S 221 " pdb=" C LEU S 221 " ideal model delta sigma weight residual 108.73 96.93 11.80 1.63e+00 3.76e-01 5.24e+01 ... (remaining 11544 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4324 17.94 - 35.88: 498 35.88 - 53.81: 120 53.81 - 71.75: 22 71.75 - 89.69: 5 Dihedral angle restraints: 4969 sinusoidal: 1757 harmonic: 3212 Sorted by residual: dihedral pdb=" CA THR R 700 " pdb=" C THR R 700 " pdb=" N SER R 701 " pdb=" CA SER R 701 " ideal model delta harmonic sigma weight residual 180.00 154.56 25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 50.64 42.36 1 1.00e+01 1.00e-02 2.51e+01 dihedral pdb=" CA GLY R 699 " pdb=" C GLY R 699 " pdb=" N THR R 700 " pdb=" CA THR R 700 " ideal model delta harmonic sigma weight residual 180.00 155.82 24.18 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 4966 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.108: 1308 0.108 - 0.216: 42 0.216 - 0.324: 4 0.324 - 0.432: 2 0.432 - 0.540: 1 Chirality restraints: 1357 Sorted by residual: chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 1.97 0.54 2.00e-01 2.50e+01 7.30e+00 chirality pdb=" CB THR R 700 " pdb=" CA THR R 700 " pdb=" OG1 THR R 700 " pdb=" CG2 THR R 700 " both_signs ideal model delta sigma weight residual False 2.55 2.19 0.36 2.00e-01 2.50e+01 3.20e+00 chirality pdb=" C10 DHT R 901 " pdb=" C1 DHT R 901 " pdb=" C5 DHT R 901 " pdb=" C9 DHT R 901 " both_signs ideal model delta sigma weight residual False -2.97 -2.62 -0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1354 not shown) Planarity restraints: 1457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL S 214 " -0.020 2.00e-02 2.50e+03 3.87e-02 1.50e+01 pdb=" C VAL S 214 " 0.067 2.00e-02 2.50e+03 pdb=" O VAL S 214 " -0.025 2.00e-02 2.50e+03 pdb=" N TYR S 215 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER S 144 " -0.012 2.00e-02 2.50e+03 2.49e-02 6.18e+00 pdb=" C SER S 144 " 0.043 2.00e-02 2.50e+03 pdb=" O SER S 144 " -0.016 2.00e-02 2.50e+03 pdb=" N ILE S 145 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR R 630 " 0.041 5.00e-02 4.00e+02 6.18e-02 6.12e+00 pdb=" N PRO R 631 " -0.107 5.00e-02 4.00e+02 pdb=" CA PRO R 631 " 0.029 5.00e-02 4.00e+02 pdb=" CD PRO R 631 " 0.036 5.00e-02 4.00e+02 ... (remaining 1454 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 578 2.73 - 3.27: 8273 3.27 - 3.81: 14017 3.81 - 4.36: 16675 4.36 - 4.90: 28635 Nonbonded interactions: 68178 Sorted by model distance: nonbonded pdb=" OG SER A 205 " pdb=" N GLY A 206 " model vdw 2.181 3.120 nonbonded pdb=" OH TYR S 60 " pdb=" O PHE S 68 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASN A 292 " pdb=" N LYS A 293 " model vdw 2.246 3.120 nonbonded pdb=" OG SER B 74 " pdb=" OD1 ASP B 76 " model vdw 2.247 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.273 3.040 ... (remaining 68173 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.650 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.920 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 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 : 0.007 0.313 8469 Z= 0.480 Angle : 0.888 19.078 11553 Z= 0.515 Chirality : 0.051 0.540 1357 Planarity : 0.005 0.062 1457 Dihedral : 16.437 89.689 2891 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 13.35 Ramachandran Plot: Outliers : 0.82 % Allowed : 7.50 % Favored : 91.67 % Rotamer: Outliers : 4.62 % Allowed : 25.24 % Favored : 70.14 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1093 helix: 0.03 (0.29), residues: 364 sheet: -0.37 (0.33), residues: 269 loop : -1.84 (0.28), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP R 714 HIS 0.010 0.001 HIS S 220 PHE 0.012 0.001 PHE R 775 TYR 0.020 0.001 TYR S 223 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.22695 ( 359) hydrogen bonds : angle 8.53026 ( 1026) SS BOND : bond 0.22152 ( 2) SS BOND : angle 12.15126 ( 4) covalent geometry : bond 0.00631 ( 8467) covalent geometry : angle 0.85870 (11549) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 191 time to evaluate : 0.904 Fit side-chains revert: symmetry clash REVERT: S 215 TYR cc_start: 0.7803 (OUTLIER) cc_final: 0.7529 (m-10) REVERT: R 706 LEU cc_start: 0.8317 (OUTLIER) cc_final: 0.7945 (tp) REVERT: R 707 SER cc_start: 0.8257 (m) cc_final: 0.8025 (p) REVERT: A 290 PHE cc_start: 0.7860 (m-10) cc_final: 0.7643 (m-10) outliers start: 39 outliers final: 16 residues processed: 212 average time/residue: 0.7919 time to fit residues: 183.2350 Evaluate side-chains 198 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 180 time to evaluate : 0.990 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 79 LEU Chi-restraints excluded: chain S residue 82 GLN Chi-restraints excluded: chain S residue 91 THR Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 215 TYR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 261 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 91 optimal weight: 0.8980 chunk 81 optimal weight: 0.2980 chunk 45 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 84 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 82 GLN S 182 ASN S 219 GLN B 110 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN G 59 ASN ** R 640 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 795 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.132083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.114523 restraints weight = 12357.293| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.07 r_work: 0.3434 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7748 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8469 Z= 0.184 Angle : 0.644 9.700 11553 Z= 0.334 Chirality : 0.045 0.346 1357 Planarity : 0.005 0.057 1457 Dihedral : 6.563 59.033 1269 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer: Outliers : 5.09 % Allowed : 20.73 % Favored : 74.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.26), residues: 1093 helix: 0.36 (0.28), residues: 367 sheet: -0.36 (0.32), residues: 271 loop : -1.85 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP R 680 HIS 0.004 0.001 HIS S 220 PHE 0.013 0.002 PHE B 278 TYR 0.023 0.002 TYR S 223 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05109 ( 359) hydrogen bonds : angle 5.53011 ( 1026) SS BOND : bond 0.00798 ( 2) SS BOND : angle 1.79371 ( 4) covalent geometry : bond 0.00406 ( 8467) covalent geometry : angle 0.64304 (11549) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 180 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8241 (m-30) cc_final: 0.7790 (m-30) REVERT: S 221 LEU cc_start: 0.7138 (tp) cc_final: 0.6524 (tp) REVERT: B 187 VAL cc_start: 0.7882 (t) cc_final: 0.7604 (p) REVERT: B 314 ARG cc_start: 0.8550 (OUTLIER) cc_final: 0.7767 (ptp-170) REVERT: R 706 LEU cc_start: 0.8175 (OUTLIER) cc_final: 0.7873 (tp) REVERT: R 707 SER cc_start: 0.7907 (m) cc_final: 0.7596 (p) REVERT: A 32 LYS cc_start: 0.8336 (mtpt) cc_final: 0.8110 (ttmm) REVERT: A 33 ASP cc_start: 0.7753 (t70) cc_final: 0.7531 (t0) REVERT: A 34 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8299 (ttpt) REVERT: A 386 MET cc_start: 0.8653 (ttp) cc_final: 0.8450 (ttm) outliers start: 43 outliers final: 17 residues processed: 204 average time/residue: 0.7918 time to fit residues: 176.8325 Evaluate side-chains 192 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 99 optimal weight: 8.9990 chunk 106 optimal weight: 0.9990 chunk 100 optimal weight: 0.6980 chunk 23 optimal weight: 20.0000 chunk 7 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN S 219 GLN B 110 ASN B 230 ASN R 600 GLN R 640 HIS R 795 ASN A 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.132549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.115098 restraints weight = 12529.913| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 2.09 r_work: 0.3442 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3299 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8469 Z= 0.144 Angle : 0.606 9.683 11553 Z= 0.310 Chirality : 0.045 0.497 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.816 59.826 1252 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 4.74 % Allowed : 22.63 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.26), residues: 1093 helix: 0.68 (0.28), residues: 365 sheet: -0.51 (0.32), residues: 276 loop : -1.64 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 PHE 0.019 0.001 PHE S 200 TYR 0.018 0.001 TYR S 223 ARG 0.008 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04093 ( 359) hydrogen bonds : angle 4.99558 ( 1026) SS BOND : bond 0.00424 ( 2) SS BOND : angle 0.93105 ( 4) covalent geometry : bond 0.00314 ( 8467) covalent geometry : angle 0.60618 (11549) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 185 time to evaluate : 1.050 Fit side-chains REVERT: S 117 LEU cc_start: 0.7107 (tp) cc_final: 0.6892 (tm) REVERT: S 211 ASP cc_start: 0.8278 (m-30) cc_final: 0.7892 (m-30) REVERT: B 101 MET cc_start: 0.8534 (OUTLIER) cc_final: 0.8255 (mtm) REVERT: B 314 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7715 (ptp-170) REVERT: R 706 LEU cc_start: 0.8209 (OUTLIER) cc_final: 0.7904 (tp) REVERT: R 707 SER cc_start: 0.7998 (m) cc_final: 0.7676 (p) REVERT: R 713 ILE cc_start: 0.8150 (tp) cc_final: 0.7922 (tt) REVERT: A 33 ASP cc_start: 0.7789 (t70) cc_final: 0.7519 (t0) REVERT: A 34 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8323 (ttpt) REVERT: A 209 GLU cc_start: 0.6899 (pp20) cc_final: 0.6616 (pp20) REVERT: A 290 PHE cc_start: 0.7766 (m-10) cc_final: 0.7512 (m-10) REVERT: A 386 MET cc_start: 0.8640 (ttp) cc_final: 0.8437 (ttm) outliers start: 40 outliers final: 23 residues processed: 206 average time/residue: 0.7903 time to fit residues: 177.5370 Evaluate side-chains 206 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 180 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 738 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 61 optimal weight: 6.9990 chunk 101 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 80 optimal weight: 0.9990 chunk 74 optimal weight: 5.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 35 HIS S 182 ASN B 110 ASN B 155 ASN B 230 ASN R 600 GLN R 795 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.129033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.111575 restraints weight = 12468.524| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 2.04 r_work: 0.3394 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 8469 Z= 0.275 Angle : 0.677 9.957 11553 Z= 0.352 Chirality : 0.047 0.328 1357 Planarity : 0.005 0.050 1457 Dihedral : 6.120 58.915 1252 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.60 % Favored : 91.31 % Rotamer: Outliers : 5.81 % Allowed : 22.87 % Favored : 71.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.26), residues: 1093 helix: 0.44 (0.28), residues: 368 sheet: -0.68 (0.32), residues: 283 loop : -1.67 (0.30), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 211 HIS 0.005 0.001 HIS S 35 PHE 0.022 0.002 PHE B 278 TYR 0.023 0.002 TYR S 223 ARG 0.008 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04595 ( 359) hydrogen bonds : angle 5.15129 ( 1026) SS BOND : bond 0.00506 ( 2) SS BOND : angle 1.12568 ( 4) covalent geometry : bond 0.00615 ( 8467) covalent geometry : angle 0.67640 (11549) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 190 time to evaluate : 0.862 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8315 (m-30) cc_final: 0.7940 (m-30) REVERT: B 101 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.8315 (mtm) REVERT: B 314 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7739 (ptp-170) REVERT: R 594 VAL cc_start: 0.7387 (OUTLIER) cc_final: 0.7116 (t) REVERT: R 706 LEU cc_start: 0.8295 (OUTLIER) cc_final: 0.7997 (tp) REVERT: R 707 SER cc_start: 0.8178 (m) cc_final: 0.7873 (p) REVERT: R 713 ILE cc_start: 0.8293 (tp) cc_final: 0.8039 (tt) REVERT: A 33 ASP cc_start: 0.7840 (t70) cc_final: 0.7575 (t0) REVERT: A 34 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8385 (ttpt) outliers start: 49 outliers final: 28 residues processed: 216 average time/residue: 0.7130 time to fit residues: 169.3759 Evaluate side-chains 216 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 176 LEU Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 594 VAL Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 70 optimal weight: 0.0070 chunk 6 optimal weight: 0.0980 chunk 93 optimal weight: 0.7980 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN B 155 ASN B 230 ASN B 259 GLN R 795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.131851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.114391 restraints weight = 12457.823| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.07 r_work: 0.3434 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8469 Z= 0.150 Angle : 0.616 8.592 11553 Z= 0.315 Chirality : 0.043 0.259 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.815 57.610 1250 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 6.40 % Allowed : 22.39 % Favored : 71.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.26), residues: 1093 helix: 0.63 (0.28), residues: 368 sheet: -0.56 (0.32), residues: 270 loop : -1.66 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS B 54 PHE 0.014 0.001 PHE S 200 TYR 0.018 0.001 TYR S 178 ARG 0.008 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 359) hydrogen bonds : angle 4.89931 ( 1026) SS BOND : bond 0.00411 ( 2) SS BOND : angle 0.87203 ( 4) covalent geometry : bond 0.00333 ( 8467) covalent geometry : angle 0.61594 (11549) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 189 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8281 (m-30) cc_final: 0.7874 (m-30) REVERT: S 219 GLN cc_start: 0.7355 (OUTLIER) cc_final: 0.6991 (pt0) REVERT: B 314 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7782 (ptp-170) REVERT: R 623 PHE cc_start: 0.8199 (t80) cc_final: 0.7941 (t80) REVERT: R 706 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7906 (tp) REVERT: R 707 SER cc_start: 0.8124 (m) cc_final: 0.7838 (p) REVERT: R 713 ILE cc_start: 0.8186 (tp) cc_final: 0.7973 (tt) REVERT: A 33 ASP cc_start: 0.7855 (t70) cc_final: 0.7567 (t0) REVERT: A 290 PHE cc_start: 0.7770 (m-10) cc_final: 0.7541 (m-10) outliers start: 54 outliers final: 32 residues processed: 217 average time/residue: 0.8137 time to fit residues: 192.2813 Evaluate side-chains 218 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 183 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 4 LEU Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 38 optimal weight: 0.0770 chunk 66 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 56 optimal weight: 10.0000 chunk 33 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 106 optimal weight: 0.0870 chunk 3 optimal weight: 3.9990 overall best weight: 0.3116 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN B 155 ASN B 259 GLN B 340 ASN R 600 GLN R 795 ASN A 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116617 restraints weight = 12469.252| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 2.09 r_work: 0.3466 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7706 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 8469 Z= 0.110 Angle : 0.581 9.445 11553 Z= 0.296 Chirality : 0.041 0.215 1357 Planarity : 0.004 0.047 1457 Dihedral : 5.541 56.759 1250 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 5.45 % Allowed : 23.93 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.26), residues: 1093 helix: 0.85 (0.29), residues: 369 sheet: -0.43 (0.33), residues: 274 loop : -1.62 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 PHE 0.013 0.001 PHE S 200 TYR 0.018 0.001 TYR S 178 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.03260 ( 359) hydrogen bonds : angle 4.61205 ( 1026) SS BOND : bond 0.00326 ( 2) SS BOND : angle 0.68292 ( 4) covalent geometry : bond 0.00239 ( 8467) covalent geometry : angle 0.58126 (11549) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 177 time to evaluate : 0.924 Fit side-chains REVERT: S 211 ASP cc_start: 0.8267 (m-30) cc_final: 0.7897 (m-30) REVERT: S 219 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7063 (pp30) REVERT: B 314 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.7755 (ptp-170) REVERT: R 623 PHE cc_start: 0.8057 (t80) cc_final: 0.7749 (t80) REVERT: R 647 PHE cc_start: 0.8414 (OUTLIER) cc_final: 0.8138 (m-10) REVERT: R 706 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7882 (tp) REVERT: R 707 SER cc_start: 0.8149 (m) cc_final: 0.7859 (p) REVERT: R 713 ILE cc_start: 0.8257 (tp) cc_final: 0.8025 (tt) REVERT: A 33 ASP cc_start: 0.7912 (t70) cc_final: 0.7576 (t0) REVERT: A 209 GLU cc_start: 0.6906 (pp20) cc_final: 0.6503 (pp20) REVERT: A 290 PHE cc_start: 0.7773 (m-10) cc_final: 0.7499 (m-10) outliers start: 46 outliers final: 23 residues processed: 202 average time/residue: 0.8710 time to fit residues: 190.7320 Evaluate side-chains 201 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 174 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 642 PHE Chi-restraints excluded: chain R residue 647 PHE Chi-restraints excluded: chain R residue 706 LEU Chi-restraints excluded: chain R residue 722 PHE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 79 optimal weight: 0.0970 chunk 81 optimal weight: 1.9990 chunk 28 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 53 optimal weight: 7.9990 chunk 9 optimal weight: 7.9990 chunk 11 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 105 optimal weight: 8.9990 chunk 82 optimal weight: 1.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN B 155 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 5 ASN R 600 GLN R 795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.130452 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112757 restraints weight = 12427.767| |-----------------------------------------------------------------------------| r_work (start): 0.3510 rms_B_bonded: 2.08 r_work: 0.3404 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3259 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 8469 Z= 0.223 Angle : 0.679 12.526 11553 Z= 0.342 Chirality : 0.045 0.266 1357 Planarity : 0.005 0.049 1457 Dihedral : 5.803 55.377 1249 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.45 % Allowed : 25.24 % Favored : 69.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.26), residues: 1093 helix: 0.74 (0.28), residues: 361 sheet: -0.48 (0.32), residues: 282 loop : -1.71 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP B 169 HIS 0.004 0.001 HIS S 220 PHE 0.017 0.002 PHE S 200 TYR 0.016 0.002 TYR S 223 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.04094 ( 359) hydrogen bonds : angle 4.88155 ( 1026) SS BOND : bond 0.00389 ( 2) SS BOND : angle 0.90426 ( 4) covalent geometry : bond 0.00502 ( 8467) covalent geometry : angle 0.67867 (11549) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 190 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: S 60 TYR cc_start: 0.8087 (m-80) cc_final: 0.7619 (m-80) REVERT: S 211 ASP cc_start: 0.8328 (m-30) cc_final: 0.7931 (m-30) REVERT: S 219 GLN cc_start: 0.7362 (OUTLIER) cc_final: 0.7010 (pt0) REVERT: B 314 ARG cc_start: 0.8538 (OUTLIER) cc_final: 0.7746 (ptp-170) REVERT: R 623 PHE cc_start: 0.8206 (t80) cc_final: 0.7884 (t80) REVERT: R 713 ILE cc_start: 0.8315 (tp) cc_final: 0.8048 (tt) REVERT: A 33 ASP cc_start: 0.7898 (t70) cc_final: 0.7585 (t0) outliers start: 46 outliers final: 27 residues processed: 218 average time/residue: 0.8059 time to fit residues: 191.9312 Evaluate side-chains 218 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 99 optimal weight: 0.1980 chunk 43 optimal weight: 4.9990 chunk 46 optimal weight: 0.6980 chunk 48 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 7.9990 chunk 57 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 35 HIS S 182 ASN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 225 HIS R 795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.130024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.112478 restraints weight = 12555.951| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 2.08 r_work: 0.3405 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 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 0.043 8469 Z= 0.219 Angle : 0.673 12.698 11553 Z= 0.342 Chirality : 0.044 0.270 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.637 53.674 1247 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.78 % Favored : 92.13 % Rotamer: Outliers : 5.09 % Allowed : 25.95 % Favored : 68.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.26), residues: 1093 helix: 0.71 (0.28), residues: 361 sheet: -0.53 (0.32), residues: 282 loop : -1.76 (0.29), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 234 HIS 0.006 0.001 HIS B 225 PHE 0.022 0.002 PHE S 200 TYR 0.021 0.002 TYR S 102 ARG 0.009 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.04035 ( 359) hydrogen bonds : angle 4.89356 ( 1026) SS BOND : bond 0.00400 ( 2) SS BOND : angle 0.88854 ( 4) covalent geometry : bond 0.00494 ( 8467) covalent geometry : angle 0.67332 (11549) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 185 time to evaluate : 1.009 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8308 (m-30) cc_final: 0.7918 (m-30) REVERT: S 219 GLN cc_start: 0.7351 (OUTLIER) cc_final: 0.7009 (pt0) REVERT: B 314 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7758 (ptp-170) REVERT: R 623 PHE cc_start: 0.8217 (t80) cc_final: 0.7888 (t80) REVERT: A 33 ASP cc_start: 0.7878 (t70) cc_final: 0.7574 (t0) outliers start: 43 outliers final: 32 residues processed: 208 average time/residue: 0.8203 time to fit residues: 186.2933 Evaluate side-chains 216 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 182 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 578 VAL Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 642 PHE Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 48 optimal weight: 0.8980 chunk 91 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 101 optimal weight: 0.9990 chunk 93 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.0570 chunk 18 optimal weight: 0.0020 chunk 24 optimal weight: 7.9990 overall best weight: 0.5108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN R 795 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.133139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.115586 restraints weight = 12584.769| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 2.11 r_work: 0.3453 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3308 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3308 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8469 Z= 0.127 Angle : 0.644 14.640 11553 Z= 0.319 Chirality : 0.042 0.218 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.298 51.457 1247 Min Nonbonded Distance : 2.330 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.41 % Favored : 92.50 % Rotamer: Outliers : 4.74 % Allowed : 27.13 % Favored : 68.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.26), residues: 1093 helix: 0.95 (0.29), residues: 361 sheet: -0.50 (0.32), residues: 279 loop : -1.70 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 234 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE S 200 TYR 0.019 0.001 TYR B 124 ARG 0.009 0.001 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.03386 ( 359) hydrogen bonds : angle 4.66631 ( 1026) SS BOND : bond 0.00419 ( 2) SS BOND : angle 0.76749 ( 4) covalent geometry : bond 0.00281 ( 8467) covalent geometry : angle 0.64355 (11549) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.879 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8277 (m-30) cc_final: 0.7888 (m-30) REVERT: S 219 GLN cc_start: 0.7314 (OUTLIER) cc_final: 0.6997 (pt0) REVERT: B 277 SER cc_start: 0.8291 (p) cc_final: 0.8072 (t) REVERT: B 314 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.7767 (ptp-170) REVERT: R 623 PHE cc_start: 0.8102 (t80) cc_final: 0.7773 (t80) REVERT: A 33 ASP cc_start: 0.7896 (t70) cc_final: 0.7560 (t0) outliers start: 40 outliers final: 27 residues processed: 198 average time/residue: 0.8176 time to fit residues: 176.1181 Evaluate side-chains 198 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 115 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 567 SER Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 642 PHE Chi-restraints excluded: chain R residue 728 ILE Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 348 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 106 optimal weight: 0.1980 chunk 74 optimal weight: 0.0040 chunk 47 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 66 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 63 optimal weight: 0.4980 chunk 97 optimal weight: 2.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 225 HIS R 795 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.116902 restraints weight = 12441.590| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 2.08 r_work: 0.3471 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8469 Z= 0.120 Angle : 0.637 14.561 11553 Z= 0.316 Chirality : 0.042 0.201 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.132 50.171 1247 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 3.79 % Allowed : 28.91 % Favored : 67.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.26), residues: 1093 helix: 1.05 (0.29), residues: 361 sheet: -0.50 (0.31), residues: 279 loop : -1.66 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS S 35 PHE 0.020 0.001 PHE S 200 TYR 0.019 0.001 TYR B 124 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03293 ( 359) hydrogen bonds : angle 4.57171 ( 1026) SS BOND : bond 0.00395 ( 2) SS BOND : angle 0.70417 ( 4) covalent geometry : bond 0.00267 ( 8467) covalent geometry : angle 0.63715 (11549) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.927 Fit side-chains revert: symmetry clash REVERT: S 211 ASP cc_start: 0.8298 (m-30) cc_final: 0.7929 (m-30) REVERT: S 219 GLN cc_start: 0.7295 (OUTLIER) cc_final: 0.6924 (pt0) REVERT: B 49 ARG cc_start: 0.8654 (mmt-90) cc_final: 0.8447 (mmt-90) REVERT: B 277 SER cc_start: 0.8276 (p) cc_final: 0.8062 (t) REVERT: B 314 ARG cc_start: 0.8507 (OUTLIER) cc_final: 0.7826 (ptp-170) REVERT: R 623 PHE cc_start: 0.8030 (t80) cc_final: 0.7707 (t80) REVERT: A 33 ASP cc_start: 0.7860 (t70) cc_final: 0.7533 (t0) outliers start: 32 outliers final: 24 residues processed: 191 average time/residue: 0.8129 time to fit residues: 169.3015 Evaluate side-chains 199 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 173 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 34 MET Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 127 VAL Chi-restraints excluded: chain S residue 219 GLN Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 160 SER Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 314 ARG Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 617 VAL Chi-restraints excluded: chain R residue 722 PHE Chi-restraints excluded: chain R residue 740 GLN Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 36 VAL Chi-restraints excluded: chain A residue 224 VAL Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 15 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 81 optimal weight: 1.9990 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN B 110 ASN ** B 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 155 ASN B 230 ASN R 795 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.133194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.115633 restraints weight = 12476.362| |-----------------------------------------------------------------------------| r_work (start): 0.3552 rms_B_bonded: 2.09 r_work: 0.3447 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3305 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8469 Z= 0.151 Angle : 0.662 14.627 11553 Z= 0.327 Chirality : 0.043 0.216 1357 Planarity : 0.004 0.049 1457 Dihedral : 5.145 49.740 1246 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.96 % Favored : 91.95 % Rotamer: Outliers : 3.55 % Allowed : 29.98 % Favored : 66.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.26), residues: 1093 helix: 1.02 (0.28), residues: 361 sheet: -0.50 (0.31), residues: 289 loop : -1.70 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 234 HIS 0.008 0.001 HIS B 225 PHE 0.024 0.002 PHE S 200 TYR 0.019 0.002 TYR B 124 ARG 0.009 0.001 ARG A 347 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 359) hydrogen bonds : angle 4.55253 ( 1026) SS BOND : bond 0.00386 ( 2) SS BOND : angle 0.75378 ( 4) covalent geometry : bond 0.00340 ( 8467) covalent geometry : angle 0.66197 (11549) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6356.44 seconds wall clock time: 110 minutes 16.14 seconds (6616.14 seconds total)