Starting phenix.real_space_refine on Wed Sep 17 10:31:55 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iv1_60917/09_2025/9iv1_60917.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iv1_60917/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9iv1_60917/09_2025/9iv1_60917.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iv1_60917/09_2025/9iv1_60917.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iv1_60917/09_2025/9iv1_60917.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iv1_60917/09_2025/9iv1_60917.map" } resolution = 2.98 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= 0.002 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): 0.01s 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: 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: {'ARG:plan': 3, 'GLU:plan': 7, '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: {'ASP:plan': 3, 'GLN:plan1': 2, 'ARG:plan': 9, 'GLU:plan': 5, 'ASN:plan1': 1} 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: {'ARG:plan': 2, 'ASN:plan1': 1, 'GLU:plan': 2} 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, 'ARG:plan': 3, 'GLU:plan': 2, 'PHE:plan': 3, 'ASP:plan': 1, 'ASN:plan1': 1} 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: {'ASP:plan': 6, 'ASN:plan1': 1, 'GLU:plan': 8, 'ARG:plan': 3, 'TYR:plan': 1} 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: 2.17, per 1000 atoms: 0.26 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: 0.64 Conformation dependent library (CDL) restraints added in 452.4 milliseconds Enol-peptide restraints added in 1.4 microseconds 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: 0.28 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: 1.37 Time building geometry restraints manager: 0.86 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: 0.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.340 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.310 ------------------------------------------------------------------------------- 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 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: -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 ARG 0.009 0.001 ARG B 137 TYR 0.020 0.001 TYR S 223 PHE 0.012 0.001 PHE R 775 TRP 0.013 0.001 TRP R 714 HIS 0.010 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00631 ( 8467) covalent geometry : angle 0.85870 (11549) SS BOND : bond 0.22152 ( 2) SS BOND : angle 12.15126 ( 4) hydrogen bonds : bond 0.22695 ( 359) hydrogen bonds : angle 8.53026 ( 1026) *********************** 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 : 0.326 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: 0.4065 time to fit residues: 93.8937 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 : 0.325 ------------------------------------------------------------------------------- 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 49 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0670 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 106 optimal weight: 0.0970 chunk 38 optimal weight: 0.6980 overall best weight: 0.7720 ------------------------------------------------------------------------------- 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 = 0.3786 r_free = 0.3786 target = 0.133003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115420 restraints weight = 12474.879| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 2.10 r_work: 0.3445 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 8469 Z= 0.161 Angle : 0.629 9.637 11553 Z= 0.326 Chirality : 0.044 0.331 1357 Planarity : 0.005 0.057 1457 Dihedral : 6.502 59.677 1269 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.59 % Favored : 92.31 % Rotamer: Outliers : 5.21 % Allowed : 20.73 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.06 (0.26), residues: 1093 helix: 0.40 (0.28), residues: 367 sheet: -0.35 (0.32), residues: 271 loop : -1.82 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 137 TYR 0.020 0.002 TYR S 223 PHE 0.012 0.002 PHE A 212 TRP 0.014 0.001 TRP R 680 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 8467) covalent geometry : angle 0.62849 (11549) SS BOND : bond 0.00600 ( 2) SS BOND : angle 1.77416 ( 4) hydrogen bonds : bond 0.04849 ( 359) hydrogen bonds : angle 5.46959 ( 1026) *********************** 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 228 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 184 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: S 103 TYR cc_start: 0.8067 (t80) cc_final: 0.7689 (t80) REVERT: S 221 LEU cc_start: 0.7138 (tp) cc_final: 0.6432 (tp) REVERT: B 187 VAL cc_start: 0.7871 (t) cc_final: 0.7602 (p) REVERT: B 314 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.7761 (ptp-170) REVERT: R 706 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7901 (tp) REVERT: R 707 SER cc_start: 0.7870 (m) cc_final: 0.7571 (p) REVERT: A 32 LYS cc_start: 0.8337 (mtpt) cc_final: 0.8114 (ttmm) REVERT: A 33 ASP cc_start: 0.7750 (t70) cc_final: 0.7520 (t0) REVERT: A 34 LYS cc_start: 0.8546 (ttpt) cc_final: 0.8298 (ttpt) REVERT: A 290 PHE cc_start: 0.7790 (m-10) cc_final: 0.7473 (m-10) outliers start: 44 outliers final: 18 residues processed: 207 average time/residue: 0.4133 time to fit residues: 93.1869 Evaluate side-chains 195 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.310 ------------------------------------------------------------------------------- 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 61 MET 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 42 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 26 optimal weight: 0.0070 chunk 88 optimal weight: 2.9990 chunk 107 optimal weight: 0.5980 chunk 100 optimal weight: 0.0970 chunk 31 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 77 optimal weight: 1.9990 chunk 56 optimal weight: 20.0000 chunk 105 optimal weight: 1.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- 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 ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 340 ASN R 600 GLN R 640 HIS A 220 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3785 r_free = 0.3785 target = 0.133090 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.115637 restraints weight = 12549.825| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.10 r_work: 0.3451 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 8469 Z= 0.139 Angle : 0.614 9.875 11553 Z= 0.311 Chirality : 0.045 0.502 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.754 59.548 1252 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 4.62 % Allowed : 22.27 % Favored : 73.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.89 (0.26), residues: 1093 helix: 0.69 (0.28), residues: 365 sheet: -0.53 (0.32), residues: 276 loop : -1.67 (0.29), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.019 0.001 TYR S 223 PHE 0.011 0.001 PHE B 234 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 8467) covalent geometry : angle 0.61383 (11549) SS BOND : bond 0.00420 ( 2) SS BOND : angle 0.99588 ( 4) hydrogen bonds : bond 0.04038 ( 359) hydrogen bonds : angle 4.99250 ( 1026) *********************** 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: 39 poor density : 186 time to evaluate : 0.336 Fit side-chains REVERT: S 103 TYR cc_start: 0.8096 (t80) cc_final: 0.7683 (t80) REVERT: B 101 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.8215 (mtm) REVERT: B 314 ARG cc_start: 0.8526 (OUTLIER) cc_final: 0.7715 (ptp-170) REVERT: R 635 MET cc_start: 0.7754 (tmm) cc_final: 0.7552 (tmm) REVERT: R 706 LEU cc_start: 0.8189 (OUTLIER) cc_final: 0.7861 (tp) REVERT: R 707 SER cc_start: 0.7979 (m) cc_final: 0.7623 (p) REVERT: A 32 LYS cc_start: 0.8349 (mtpt) cc_final: 0.8134 (ttmm) REVERT: A 33 ASP cc_start: 0.7789 (t70) cc_final: 0.7528 (t0) REVERT: A 34 LYS cc_start: 0.8567 (ttpt) cc_final: 0.8298 (ttpt) REVERT: A 209 GLU cc_start: 0.6883 (pp20) cc_final: 0.6580 (pp20) REVERT: A 290 PHE cc_start: 0.7755 (m-10) cc_final: 0.7427 (m-10) outliers start: 39 outliers final: 21 residues processed: 204 average time/residue: 0.4205 time to fit residues: 93.4895 Evaluate side-chains 198 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 174 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 115 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 128 THR 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 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 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 18 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 107 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 106 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 19 optimal weight: 8.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 ** S 219 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN B 230 ASN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3761 r_free = 0.3761 target = 0.131440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.113939 restraints weight = 12605.568| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 2.10 r_work: 0.3428 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3283 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7764 moved from start: 0.1803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8469 Z= 0.190 Angle : 0.624 10.083 11553 Z= 0.320 Chirality : 0.045 0.331 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.876 59.704 1252 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 5.45 % Allowed : 22.27 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.91 (0.26), residues: 1093 helix: 0.65 (0.28), residues: 366 sheet: -0.54 (0.31), residues: 281 loop : -1.66 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 137 TYR 0.018 0.002 TYR S 102 PHE 0.015 0.002 PHE B 278 TRP 0.012 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 8467) covalent geometry : angle 0.62388 (11549) SS BOND : bond 0.00473 ( 2) SS BOND : angle 0.99855 ( 4) hydrogen bonds : bond 0.04119 ( 359) hydrogen bonds : angle 4.95608 ( 1026) *********************** 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 227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 103 TYR cc_start: 0.8157 (t80) cc_final: 0.7709 (t80) REVERT: B 314 ARG cc_start: 0.8544 (OUTLIER) cc_final: 0.7719 (ptp-170) REVERT: R 706 LEU cc_start: 0.8194 (OUTLIER) cc_final: 0.7843 (tp) REVERT: R 707 SER cc_start: 0.8100 (m) cc_final: 0.7690 (p) REVERT: A 32 LYS cc_start: 0.8351 (mtpt) cc_final: 0.8137 (ttmm) REVERT: A 33 ASP cc_start: 0.7795 (t70) cc_final: 0.7537 (t0) REVERT: A 34 LYS cc_start: 0.8542 (ttpt) cc_final: 0.8267 (ttpt) REVERT: A 290 PHE cc_start: 0.7756 (m-10) cc_final: 0.7432 (m-10) outliers start: 46 outliers final: 32 residues processed: 204 average time/residue: 0.4032 time to fit residues: 89.8922 Evaluate side-chains 211 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 177 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 2 VAL 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 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ASP 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 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 9 optimal weight: 6.9990 chunk 72 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 61 optimal weight: 7.9990 chunk 54 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 0.2980 chunk 87 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 182 ASN S 219 GLN B 110 ASN B 230 ASN B 259 GLN 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 = 0.3781 r_free = 0.3781 target = 0.132827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.115391 restraints weight = 12539.385| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.10 r_work: 0.3451 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3307 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3307 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.1891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 8469 Z= 0.135 Angle : 0.599 11.249 11553 Z= 0.303 Chirality : 0.043 0.254 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.742 59.275 1252 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 6.04 % Allowed : 22.87 % Favored : 71.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.78 (0.26), residues: 1093 helix: 0.82 (0.28), residues: 366 sheet: -0.47 (0.32), residues: 279 loop : -1.65 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.016 0.001 TYR S 178 PHE 0.012 0.001 PHE A 212 TRP 0.012 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 8467) covalent geometry : angle 0.59841 (11549) SS BOND : bond 0.00358 ( 2) SS BOND : angle 0.82455 ( 4) hydrogen bonds : bond 0.03624 ( 359) hydrogen bonds : angle 4.75290 ( 1026) *********************** 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 237 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 186 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: S 60 TYR cc_start: 0.7910 (m-80) cc_final: 0.7300 (m-80) REVERT: B 259 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7555 (mp10) REVERT: B 314 ARG cc_start: 0.8531 (OUTLIER) cc_final: 0.7740 (ptp-170) REVERT: R 623 PHE cc_start: 0.8141 (t80) cc_final: 0.7888 (t80) REVERT: R 706 LEU cc_start: 0.8091 (OUTLIER) cc_final: 0.7744 (tp) REVERT: R 707 SER cc_start: 0.8103 (m) cc_final: 0.7693 (p) REVERT: A 32 LYS cc_start: 0.8350 (mtpt) cc_final: 0.8138 (ttmm) REVERT: A 33 ASP cc_start: 0.7819 (t70) cc_final: 0.7551 (t0) REVERT: A 34 LYS cc_start: 0.8523 (ttpt) cc_final: 0.8248 (ttpt) REVERT: A 290 PHE cc_start: 0.7707 (m-10) cc_final: 0.7396 (m-10) outliers start: 51 outliers final: 30 residues processed: 217 average time/residue: 0.4127 time to fit residues: 97.3941 Evaluate side-chains 212 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 179 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain S residue 12 VAL 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 76 ASP 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 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 229 ILE Chi-restraints excluded: chain B residue 259 GLN 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 706 LEU Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 760 LYS 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 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 46 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 102 optimal weight: 0.2980 chunk 2 optimal weight: 3.9990 chunk 85 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 73 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 7.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 795 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.132907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.115462 restraints weight = 12433.321| |-----------------------------------------------------------------------------| r_work (start): 0.3557 rms_B_bonded: 2.09 r_work: 0.3454 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8469 Z= 0.139 Angle : 0.604 10.994 11553 Z= 0.305 Chirality : 0.043 0.261 1357 Planarity : 0.004 0.047 1457 Dihedral : 5.682 59.317 1252 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.69 % Favored : 92.22 % Rotamer: Outliers : 5.69 % Allowed : 24.29 % Favored : 70.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.78 (0.26), residues: 1093 helix: 0.79 (0.28), residues: 366 sheet: -0.46 (0.32), residues: 279 loop : -1.62 (0.30), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 137 TYR 0.017 0.001 TYR B 124 PHE 0.014 0.001 PHE R 716 TRP 0.011 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 8467) covalent geometry : angle 0.60394 (11549) SS BOND : bond 0.00412 ( 2) SS BOND : angle 0.79002 ( 4) hydrogen bonds : bond 0.03595 ( 359) hydrogen bonds : angle 4.72234 ( 1026) *********************** 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 230 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 182 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: S 60 TYR cc_start: 0.7940 (m-80) cc_final: 0.7540 (m-80) REVERT: B 314 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.7794 (ptp-170) REVERT: R 623 PHE cc_start: 0.8120 (t80) cc_final: 0.7875 (t80) REVERT: R 706 LEU cc_start: 0.8036 (OUTLIER) cc_final: 0.7717 (tp) REVERT: R 707 SER cc_start: 0.8146 (m) cc_final: 0.7799 (p) REVERT: A 33 ASP cc_start: 0.7773 (t70) cc_final: 0.7552 (t0) REVERT: A 290 PHE cc_start: 0.7699 (m-10) cc_final: 0.7400 (m-10) outliers start: 48 outliers final: 32 residues processed: 210 average time/residue: 0.4368 time to fit residues: 99.5800 Evaluate side-chains 213 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.333 ------------------------------------------------------------------------------- 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 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 76 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 127 LYS Chi-restraints excluded: chain B residue 152 LEU 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 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 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 348 ILE Chi-restraints excluded: chain A residue 383 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 14 optimal weight: 4.9990 chunk 57 optimal weight: 8.9990 chunk 58 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 104 optimal weight: 6.9990 chunk 75 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 51 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 50 optimal weight: 0.7980 overall best weight: 1.4582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** R 795 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.130135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.112622 restraints weight = 12609.023| |-----------------------------------------------------------------------------| r_work (start): 0.3514 rms_B_bonded: 2.09 r_work: 0.3409 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7787 moved from start: 0.2134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 8469 Z= 0.233 Angle : 0.664 11.133 11553 Z= 0.337 Chirality : 0.045 0.276 1357 Planarity : 0.005 0.048 1457 Dihedral : 5.949 58.502 1252 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.51 % Favored : 91.40 % Rotamer: Outliers : 5.57 % Allowed : 25.36 % Favored : 69.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.86 (0.26), residues: 1093 helix: 0.71 (0.28), residues: 360 sheet: -0.46 (0.32), residues: 272 loop : -1.65 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 49 TYR 0.019 0.002 TYR S 223 PHE 0.018 0.002 PHE B 278 TRP 0.012 0.002 TRP B 211 HIS 0.006 0.001 HIS S 220 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 8467) covalent geometry : angle 0.66397 (11549) SS BOND : bond 0.00417 ( 2) SS BOND : angle 0.92505 ( 4) hydrogen bonds : bond 0.04163 ( 359) hydrogen bonds : angle 4.89593 ( 1026) *********************** 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 238 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 191 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: S 117 LEU cc_start: 0.7373 (tp) cc_final: 0.7115 (tp) REVERT: B 230 ASN cc_start: 0.8442 (m-40) cc_final: 0.8227 (m-40) REVERT: B 259 GLN cc_start: 0.8495 (mp10) cc_final: 0.7657 (mp10) REVERT: B 314 ARG cc_start: 0.8524 (OUTLIER) cc_final: 0.7687 (ptp-170) REVERT: R 623 PHE cc_start: 0.8247 (t80) cc_final: 0.7977 (t80) REVERT: R 706 LEU cc_start: 0.8121 (OUTLIER) cc_final: 0.7794 (tp) REVERT: R 707 SER cc_start: 0.8219 (m) cc_final: 0.7876 (p) REVERT: A 33 ASP cc_start: 0.7798 (t70) cc_final: 0.7574 (t0) REVERT: A 290 PHE cc_start: 0.7723 (m-10) cc_final: 0.7369 (m-10) outliers start: 47 outliers final: 32 residues processed: 217 average time/residue: 0.3891 time to fit residues: 92.6880 Evaluate side-chains 218 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 0.326 ------------------------------------------------------------------------------- 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 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ASP 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 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 760 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 39 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 25 optimal weight: 0.0470 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 57 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 75 optimal weight: 6.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- 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 225 HIS B 259 GLN R 795 ASN A 220 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.132263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.114847 restraints weight = 12524.624| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 2.10 r_work: 0.3437 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3292 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.3292 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.2146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 8469 Z= 0.143 Angle : 0.619 11.863 11553 Z= 0.313 Chirality : 0.042 0.237 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.746 59.781 1252 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.50 % Favored : 92.41 % Rotamer: Outliers : 4.98 % Allowed : 26.42 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.80 (0.26), residues: 1093 helix: 0.87 (0.28), residues: 359 sheet: -0.49 (0.32), residues: 281 loop : -1.68 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 137 TYR 0.019 0.002 TYR B 124 PHE 0.013 0.001 PHE S 200 TRP 0.012 0.001 TRP B 169 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8467) covalent geometry : angle 0.61915 (11549) SS BOND : bond 0.00416 ( 2) SS BOND : angle 0.85670 ( 4) hydrogen bonds : bond 0.03594 ( 359) hydrogen bonds : angle 4.73216 ( 1026) *********************** 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 227 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 185 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: S 59 TYR cc_start: 0.8591 (m-80) cc_final: 0.8313 (m-10) REVERT: S 117 LEU cc_start: 0.7255 (tp) cc_final: 0.7038 (tp) REVERT: B 200 VAL cc_start: 0.8254 (m) cc_final: 0.8049 (t) REVERT: B 314 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7744 (ptp-170) REVERT: R 623 PHE cc_start: 0.8173 (t80) cc_final: 0.7866 (t80) REVERT: R 706 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7677 (tp) REVERT: R 707 SER cc_start: 0.8174 (m) cc_final: 0.7820 (p) REVERT: A 33 ASP cc_start: 0.7855 (t70) cc_final: 0.7515 (t0) REVERT: A 209 GLU cc_start: 0.7017 (pp20) cc_final: 0.6680 (pp20) REVERT: A 290 PHE cc_start: 0.7697 (m-10) cc_final: 0.7373 (m-10) REVERT: A 331 ASP cc_start: 0.7119 (t0) cc_final: 0.6845 (t0) outliers start: 42 outliers final: 34 residues processed: 205 average time/residue: 0.4371 time to fit residues: 97.2441 Evaluate side-chains 212 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 176 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 176 LEU Chi-restraints excluded: chain B residue 43 ILE Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 101 MET Chi-restraints excluded: chain B residue 146 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 259 GLN 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 722 PHE Chi-restraints excluded: chain R residue 732 ILE Chi-restraints excluded: chain R residue 757 LEU Chi-restraints excluded: chain R residue 760 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 0.0470 chunk 97 optimal weight: 2.9990 chunk 70 optimal weight: 0.0980 chunk 12 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 0.7980 chunk 51 optimal weight: 0.6980 chunk 77 optimal weight: 0.0030 chunk 102 optimal weight: 0.0370 chunk 1 optimal weight: 5.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.1366 ------------------------------------------------------------------------------- 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 G 5 ASN G 59 ASN R 600 GLN R 795 ASN A 220 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.135751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.118421 restraints weight = 12577.677| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.11 r_work: 0.3490 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.2316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 8469 Z= 0.107 Angle : 0.612 11.680 11553 Z= 0.307 Chirality : 0.042 0.204 1357 Planarity : 0.004 0.047 1457 Dihedral : 5.504 59.129 1252 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.95 % Favored : 92.96 % Rotamer: Outliers : 4.62 % Allowed : 27.13 % Favored : 68.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.69 (0.26), residues: 1093 helix: 0.90 (0.29), residues: 367 sheet: -0.42 (0.32), residues: 274 loop : -1.59 (0.30), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 137 TYR 0.018 0.001 TYR S 178 PHE 0.021 0.001 PHE A 212 TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00232 ( 8467) covalent geometry : angle 0.61218 (11549) SS BOND : bond 0.00397 ( 2) SS BOND : angle 0.72951 ( 4) hydrogen bonds : bond 0.03145 ( 359) hydrogen bonds : angle 4.53142 ( 1026) *********************** 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 220 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 181 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: S 59 TYR cc_start: 0.8523 (m-80) cc_final: 0.8227 (m-10) REVERT: S 115 THR cc_start: 0.8018 (OUTLIER) cc_final: 0.7802 (p) REVERT: R 623 PHE cc_start: 0.8029 (t80) cc_final: 0.7726 (t80) REVERT: R 706 LEU cc_start: 0.7814 (OUTLIER) cc_final: 0.7554 (tp) REVERT: R 707 SER cc_start: 0.8113 (m) cc_final: 0.7805 (p) REVERT: A 33 ASP cc_start: 0.7875 (t70) cc_final: 0.7555 (t0) REVERT: A 51 SER cc_start: 0.8363 (p) cc_final: 0.8052 (t) outliers start: 39 outliers final: 23 residues processed: 205 average time/residue: 0.4315 time to fit residues: 96.3256 Evaluate side-chains 202 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 177 time to evaluate : 0.341 ------------------------------------------------------------------------------- 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 B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR 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 259 GLN Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 318 LEU Chi-restraints excluded: chain B residue 325 MET 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 642 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 760 LYS Chi-restraints excluded: chain R residue 778 LEU Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 272 ASP Chi-restraints excluded: chain A residue 315 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 73 optimal weight: 1.9990 chunk 63 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 42 optimal weight: 0.4980 chunk 101 optimal weight: 0.0670 chunk 64 optimal weight: 3.9990 chunk 26 optimal weight: 0.8980 chunk 95 optimal weight: 4.9990 chunk 88 optimal weight: 2.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 G 59 ASN R 600 GLN R 795 ASN A 390 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.134142 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.116627 restraints weight = 12537.429| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 2.10 r_work: 0.3461 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3318 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7710 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8469 Z= 0.135 Angle : 0.631 11.052 11553 Z= 0.319 Chirality : 0.043 0.235 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.400 57.563 1249 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 3.20 % Allowed : 29.27 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -0.65 (0.26), residues: 1093 helix: 1.01 (0.29), residues: 360 sheet: -0.37 (0.31), residues: 288 loop : -1.66 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 347 TYR 0.016 0.001 TYR S 178 PHE 0.020 0.001 PHE A 212 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 8467) covalent geometry : angle 0.63136 (11549) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.72929 ( 4) hydrogen bonds : bond 0.03420 ( 359) hydrogen bonds : angle 4.58171 ( 1026) ********************** 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 204 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 177 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: S 59 TYR cc_start: 0.8543 (m-80) cc_final: 0.8292 (m-10) REVERT: R 623 PHE cc_start: 0.8038 (t80) cc_final: 0.7692 (t80) REVERT: R 706 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7596 (tp) REVERT: R 707 SER cc_start: 0.8149 (m) cc_final: 0.7839 (p) REVERT: A 33 ASP cc_start: 0.7825 (t70) cc_final: 0.7509 (t0) REVERT: A 51 SER cc_start: 0.8441 (p) cc_final: 0.8204 (t) REVERT: A 290 PHE cc_start: 0.7744 (m-10) cc_final: 0.7386 (m-10) REVERT: A 331 ASP cc_start: 0.7255 (t0) cc_final: 0.6934 (t70) REVERT: A 346 LEU cc_start: 0.8267 (mm) cc_final: 0.8059 (mt) REVERT: A 393 LEU cc_start: 0.8322 (mt) cc_final: 0.8062 (mt) outliers start: 27 outliers final: 20 residues processed: 191 average time/residue: 0.4066 time to fit residues: 85.1408 Evaluate side-chains 187 residues out of total 943 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 166 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 B residue 43 ILE Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 LEU Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 276 VAL 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 617 VAL Chi-restraints excluded: chain R residue 642 PHE Chi-restraints excluded: chain R residue 706 LEU 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 315 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 68 optimal weight: 0.8980 chunk 23 optimal weight: 20.0000 chunk 48 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 2 optimal weight: 0.5980 chunk 80 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.0970 chunk 34 optimal weight: 0.0020 chunk 42 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 overall best weight: 0.3986 ------------------------------------------------------------------------------- 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 G 59 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 = 0.3812 r_free = 0.3812 target = 0.135166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.117608 restraints weight = 12553.972| |-----------------------------------------------------------------------------| r_work (start): 0.3580 rms_B_bonded: 2.12 r_work: 0.3477 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3335 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8469 Z= 0.119 Angle : 0.628 10.861 11553 Z= 0.313 Chirality : 0.042 0.238 1357 Planarity : 0.004 0.048 1457 Dihedral : 5.299 57.425 1249 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.14 % Favored : 92.77 % Rotamer: Outliers : 2.96 % Allowed : 30.57 % 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 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: -0.61 (0.26), residues: 1093 helix: 1.07 (0.29), residues: 360 sheet: -0.40 (0.31), residues: 278 loop : -1.60 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 347 TYR 0.016 0.001 TYR S 178 PHE 0.019 0.001 PHE A 212 TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 8467) covalent geometry : angle 0.62819 (11549) SS BOND : bond 0.00341 ( 2) SS BOND : angle 0.72092 ( 4) hydrogen bonds : bond 0.03296 ( 359) hydrogen bonds : angle 4.51479 ( 1026) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3448.77 seconds wall clock time: 59 minutes 41.70 seconds (3581.70 seconds total)