Starting phenix.real_space_refine on Wed Mar 12 02:03:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.cif Found real_map, /net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.map" model { file = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7xn6_33312/03_2025/7xn6_33312.cif" } resolution = 3.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 38 5.16 5 C 4346 2.51 5 N 1211 2.21 5 O 1277 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 6874 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1714 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 6, 'TRANS': 204} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3256 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 13, 'TRANS': 408} Chain: "C" Number of atoms: 1394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1394 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 6, 'TRANS': 163} Chain breaks: 5 Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 466 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 35 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 35 Unusual residues: {'APR': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'NCA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.06, per 1000 atoms: 0.74 Number of scatterers: 6874 At special positions: 0 Unit cell: (107.776, 96.83, 76.622, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 38 16.00 P 2 15.00 O 1277 8.00 N 1211 7.00 C 4346 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.86 Conformation dependent library (CDL) restraints added in 1.0 seconds 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1606 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 5 sheets defined 42.3% alpha, 8.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'A' and resid 67 through 80 Processing helix chain 'A' and resid 92 through 105 Processing helix chain 'A' and resid 136 through 141 removed outlier: 3.541A pdb=" N THR A 140 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 214 through 226 removed outlier: 4.355A pdb=" N CYS A 220 " --> pdb=" O ILE A 216 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN A 225 " --> pdb=" O ALA A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 243 Processing helix chain 'B' and resid 52 through 74 removed outlier: 4.209A pdb=" N PHE B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N LYS B 61 " --> pdb=" O ALA B 57 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN B 66 " --> pdb=" O ALA B 62 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER B 67 " --> pdb=" O VAL B 63 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N LEU B 70 " --> pdb=" O GLN B 66 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N MET B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 75 through 82 removed outlier: 3.547A pdb=" N GLU B 79 " --> pdb=" O GLY B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 93 through 114 removed outlier: 3.927A pdb=" N LEU B 99 " --> pdb=" O ALA B 95 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL B 110 " --> pdb=" O ASN B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 128 Processing helix chain 'B' and resid 153 through 158 Processing helix chain 'B' and resid 171 through 176 removed outlier: 3.568A pdb=" N LEU B 175 " --> pdb=" O GLY B 171 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LEU B 176 " --> pdb=" O ASP B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 171 through 176' Processing helix chain 'B' and resid 218 through 222 removed outlier: 3.570A pdb=" N CYS B 221 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ARG B 222 " --> pdb=" O PRO B 219 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 218 through 222' Processing helix chain 'B' and resid 244 through 251 removed outlier: 3.715A pdb=" N VAL B 248 " --> pdb=" O HIS B 244 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 256 removed outlier: 4.035A pdb=" N GLY B 255 " --> pdb=" O PHE B 251 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA B 256 " --> pdb=" O PRO B 252 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 251 through 256' Processing helix chain 'B' and resid 280 through 292 removed outlier: 4.028A pdb=" N ALA B 284 " --> pdb=" O LYS B 280 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLU B 289 " --> pdb=" O LEU B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 302 removed outlier: 3.882A pdb=" N TYR B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 314 through 322 removed outlier: 3.800A pdb=" N SER B 320 " --> pdb=" O ARG B 316 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 355 through 363 removed outlier: 3.821A pdb=" N GLY B 361 " --> pdb=" O PRO B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 378 removed outlier: 4.148A pdb=" N THR B 371 " --> pdb=" O GLY B 367 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ASP B 378 " --> pdb=" O TRP B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 392 Processing helix chain 'B' and resid 409 through 414 Processing helix chain 'B' and resid 420 through 431 Processing helix chain 'B' and resid 447 through 456 Processing helix chain 'B' and resid 457 through 468 Processing helix chain 'C' and resid 69 through 80 removed outlier: 3.783A pdb=" N GLU C 76 " --> pdb=" O ALA C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 94 through 105 Processing helix chain 'C' and resid 107 through 111 removed outlier: 4.015A pdb=" N LYS C 110 " --> pdb=" O ASP C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 141 Processing helix chain 'C' and resid 142 through 144 No H-bonds generated for 'chain 'C' and resid 142 through 144' Processing helix chain 'C' and resid 213 through 226 Processing helix chain 'C' and resid 231 through 246 Processing helix chain 'D' and resid 86 through 91 Processing helix chain 'D' and resid 102 through 112 removed outlier: 3.628A pdb=" N THR D 110 " --> pdb=" O ARG D 106 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN D 111 " --> pdb=" O HIS D 107 " (cutoff:3.500A) Processing helix chain 'D' and resid 117 through 128 removed outlier: 4.042A pdb=" N GLU D 123 " --> pdb=" O GLU D 119 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 89 removed outlier: 6.208A pdb=" N LEU A 46 " --> pdb=" O VAL A 115 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL A 117 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ILE A 48 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 7.552A pdb=" N LEU A 119 " --> pdb=" O ILE A 48 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N ILE A 50 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N PHE A 114 " --> pdb=" O LEU A 157 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N ILE A 159 " --> pdb=" O PHE A 114 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS A 116 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N LYS A 156 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N ALA A 196 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N PHE A 158 " --> pdb=" O ALA A 196 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 126 through 128 Processing sheet with id=AA3, first strand: chain 'B' and resid 225 through 227 Processing sheet with id=AA4, first strand: chain 'B' and resid 149 through 152 Processing sheet with id=AA5, first strand: chain 'C' and resid 84 through 87 removed outlier: 7.079A pdb=" N CYS C 47 " --> pdb=" O ARG C 86 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N LEU C 46 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N VAL C 117 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ILE C 48 " --> pdb=" O VAL C 117 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N LEU C 119 " --> pdb=" O ILE C 48 " (cutoff:3.500A) removed outlier: 6.004A pdb=" N ILE C 50 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU C 194 " --> pdb=" O LYS C 156 " (cutoff:3.500A) 227 hydrogen bonds defined for protein. 654 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: 1.63 Time building geometry restraints manager: 2.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 1150 1.29 - 1.42: 1879 1.42 - 1.55: 3918 1.55 - 1.68: 6 1.68 - 1.81: 64 Bond restraints: 7017 Sorted by residual: bond pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 1.397 1.573 -0.176 2.00e-02 2.50e+03 7.77e+01 bond pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 1.522 1.413 0.109 1.34e-02 5.57e+03 6.65e+01 bond pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " ideal model delta sigma weight residual 1.529 1.675 -0.146 2.00e-02 2.50e+03 5.36e+01 bond pdb=" CA ALA B 141 " pdb=" C ALA B 141 " ideal model delta sigma weight residual 1.528 1.449 0.080 1.39e-02 5.18e+03 3.28e+01 bond pdb=" CA SER B 139 " pdb=" C SER B 139 " ideal model delta sigma weight residual 1.522 1.453 0.070 1.23e-02 6.61e+03 3.20e+01 ... (remaining 7012 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.61: 9408 4.61 - 9.23: 28 9.23 - 13.84: 4 13.84 - 18.46: 3 18.46 - 23.07: 4 Bond angle restraints: 9447 Sorted by residual: angle pdb=" O3A APR A1001 " pdb=" PB APR A1001 " pdb=" O5D APR A1001 " ideal model delta sigma weight residual 101.31 124.38 -23.07 3.00e+00 1.11e-01 5.91e+01 angle pdb=" C1D APR A1001 " pdb=" C2D APR A1001 " pdb=" O2D APR A1001 " ideal model delta sigma weight residual 110.00 87.63 22.37 3.00e+00 1.11e-01 5.56e+01 angle pdb=" N TYR B 68 " pdb=" CA TYR B 68 " pdb=" C TYR B 68 " ideal model delta sigma weight residual 113.38 105.51 7.87 1.23e+00 6.61e-01 4.09e+01 angle pdb=" C5D APR A1001 " pdb=" C4D APR A1001 " pdb=" O4D APR A1001 " ideal model delta sigma weight residual 111.97 130.75 -18.78 3.00e+00 1.11e-01 3.92e+01 angle pdb=" O3A APR A1001 " pdb=" PA APR A1001 " pdb=" O5' APR A1001 " ideal model delta sigma weight residual 102.36 121.10 -18.74 3.00e+00 1.11e-01 3.90e+01 ... (remaining 9442 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 3681 17.82 - 35.64: 426 35.64 - 53.46: 89 53.46 - 71.28: 11 71.28 - 89.09: 10 Dihedral angle restraints: 4217 sinusoidal: 1729 harmonic: 2488 Sorted by residual: dihedral pdb=" CA GLU D 140 " pdb=" C GLU D 140 " pdb=" N PHE D 141 " pdb=" CA PHE D 141 " ideal model delta harmonic sigma weight residual 180.00 -152.49 -27.51 0 5.00e+00 4.00e-02 3.03e+01 dihedral pdb=" CA LYS B 300 " pdb=" C LYS B 300 " pdb=" N ALA B 301 " pdb=" CA ALA B 301 " ideal model delta harmonic sigma weight residual -180.00 -154.71 -25.29 0 5.00e+00 4.00e-02 2.56e+01 dihedral pdb=" C ASN B 355 " pdb=" N ASN B 355 " pdb=" CA ASN B 355 " pdb=" CB ASN B 355 " ideal model delta harmonic sigma weight residual -122.60 -110.04 -12.56 0 2.50e+00 1.60e-01 2.52e+01 ... (remaining 4214 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.185: 1002 0.185 - 0.370: 5 0.370 - 0.556: 1 0.556 - 0.741: 0 0.741 - 0.926: 2 Chirality restraints: 1010 Sorted by residual: chirality pdb=" C2D APR A1001 " pdb=" C1D APR A1001 " pdb=" C3D APR A1001 " pdb=" O2D APR A1001 " both_signs ideal model delta sigma weight residual False -2.45 -3.38 0.93 2.00e-01 2.50e+01 2.14e+01 chirality pdb=" C3D APR A1001 " pdb=" C2D APR A1001 " pdb=" C4D APR A1001 " pdb=" O3D APR A1001 " both_signs ideal model delta sigma weight residual False -2.71 -1.96 -0.75 2.00e-01 2.50e+01 1.40e+01 chirality pdb=" C4D APR A1001 " pdb=" C3D APR A1001 " pdb=" C5D APR A1001 " pdb=" O4D APR A1001 " both_signs ideal model delta sigma weight residual False -2.49 -2.04 -0.45 2.00e-01 2.50e+01 5.05e+00 ... (remaining 1007 not shown) Planarity restraints: 1221 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' APR A1001 " -0.124 2.00e-02 2.50e+03 5.80e-02 9.25e+01 pdb=" C2 APR A1001 " 0.007 2.00e-02 2.50e+03 pdb=" C4 APR A1001 " 0.060 2.00e-02 2.50e+03 pdb=" C5 APR A1001 " 0.057 2.00e-02 2.50e+03 pdb=" C6 APR A1001 " -0.001 2.00e-02 2.50e+03 pdb=" C8 APR A1001 " 0.016 2.00e-02 2.50e+03 pdb=" N1 APR A1001 " -0.024 2.00e-02 2.50e+03 pdb=" N3 APR A1001 " 0.051 2.00e-02 2.50e+03 pdb=" N6 APR A1001 " -0.095 2.00e-02 2.50e+03 pdb=" N7 APR A1001 " 0.046 2.00e-02 2.50e+03 pdb=" N9 APR A1001 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN B 66 " 0.024 2.00e-02 2.50e+03 4.77e-02 2.27e+01 pdb=" C GLN B 66 " -0.082 2.00e-02 2.50e+03 pdb=" O GLN B 66 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 67 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 443 " -0.016 2.00e-02 2.50e+03 3.08e-02 9.48e+00 pdb=" C ASN B 443 " 0.053 2.00e-02 2.50e+03 pdb=" O ASN B 443 " -0.019 2.00e-02 2.50e+03 pdb=" N SER B 444 " -0.018 2.00e-02 2.50e+03 ... (remaining 1218 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 4 2.26 - 2.92: 2852 2.92 - 3.58: 9411 3.58 - 4.24: 15202 4.24 - 4.90: 26010 Nonbonded interactions: 53479 Sorted by model distance: nonbonded pdb=" NE ARG A 207 " pdb=" C1D APR A1001 " model vdw 1.596 3.550 nonbonded pdb=" C3D APR A1001 " pdb=" O5D APR A1001 " model vdw 2.029 2.776 nonbonded pdb=" CZ ARG A 207 " pdb=" C1D APR A1001 " model vdw 2.227 2.960 nonbonded pdb=" OH TYR A 37 " pdb=" O GLY A 153 " model vdw 2.238 3.040 nonbonded pdb=" O PHE B 72 " pdb=" N LEU B 85 " model vdw 2.261 3.120 ... (remaining 53474 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 20.080 Find NCS groups from input model: 0.060 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 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 0.176 7017 Z= 0.457 Angle : 0.965 23.071 9447 Z= 0.518 Chirality : 0.061 0.926 1010 Planarity : 0.006 0.069 1221 Dihedral : 15.940 89.095 2611 Min Nonbonded Distance : 1.596 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.58 % Favored : 91.42 % Rotamer: Outliers : 0.70 % Allowed : 0.98 % Favored : 98.33 % Cbeta Deviations : 0.25 % 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: -3.19 (0.27), residues: 839 helix: -0.96 (0.28), residues: 342 sheet: -2.81 (0.47), residues: 119 loop : -2.98 (0.28), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP B 261 HIS 0.007 0.001 HIS A 121 PHE 0.007 0.001 PHE A 78 TYR 0.016 0.001 TYR B 68 ARG 0.007 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 130 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: B 306 GLN cc_start: 0.6926 (pp30) cc_final: 0.6716 (pp30) REVERT: B 332 MET cc_start: 0.8470 (tmm) cc_final: 0.8254 (tmm) REVERT: C 89 ASN cc_start: 0.7856 (p0) cc_final: 0.7637 (p0) REVERT: C 102 ASP cc_start: 0.7464 (m-30) cc_final: 0.6305 (m-30) outliers start: 5 outliers final: 2 residues processed: 135 average time/residue: 0.1916 time to fit residues: 34.3987 Evaluate side-chains 106 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 104 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain B residue 139 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 71 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 22 optimal weight: 0.6980 chunk 43 optimal weight: 0.0980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 121 HIS A 208 ASN A 217 GLN B 140 ASN B 200 HIS B 210 ASN B 309 GLN B 443 ASN ** C 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.139647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.110573 restraints weight = 12124.947| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 2.85 r_work: 0.3370 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7017 Z= 0.195 Angle : 0.574 5.858 9447 Z= 0.305 Chirality : 0.042 0.152 1010 Planarity : 0.005 0.066 1221 Dihedral : 7.943 78.761 986 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 1.53 % Allowed : 8.51 % Favored : 89.96 % 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: -2.72 (0.28), residues: 839 helix: -0.58 (0.28), residues: 342 sheet: -2.70 (0.47), residues: 120 loop : -2.65 (0.29), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.030 0.001 PHE A 247 TYR 0.017 0.001 TYR A 37 ARG 0.005 0.000 ARG C 75 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 110 time to evaluate : 0.810 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4529 (OUTLIER) cc_final: 0.4033 (m100) REVERT: B 302 TYR cc_start: 0.7616 (t80) cc_final: 0.7129 (t80) REVERT: C 89 ASN cc_start: 0.8163 (p0) cc_final: 0.7928 (p0) REVERT: D 140 GLU cc_start: 0.7970 (mm-30) cc_final: 0.7706 (mm-30) outliers start: 11 outliers final: 8 residues processed: 115 average time/residue: 0.2003 time to fit residues: 30.5141 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 108 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 216 ILE Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 68 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 70 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 63 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 64 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 21 optimal weight: 0.0170 overall best weight: 1.3622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.136219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.106752 restraints weight = 12661.285| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.27 r_work: 0.3304 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 7017 Z= 0.306 Angle : 0.611 6.250 9447 Z= 0.323 Chirality : 0.043 0.137 1010 Planarity : 0.005 0.062 1221 Dihedral : 7.948 78.524 985 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 1.81 % Allowed : 12.97 % Favored : 85.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.28), residues: 839 helix: -0.73 (0.27), residues: 356 sheet: -2.61 (0.46), residues: 120 loop : -2.61 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 261 HIS 0.006 0.001 HIS B 202 PHE 0.012 0.001 PHE B 299 TYR 0.023 0.002 TYR A 37 ARG 0.010 0.001 ARG A 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 113 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4541 (OUTLIER) cc_final: 0.4050 (m100) REVERT: C 89 ASN cc_start: 0.8111 (p0) cc_final: 0.7815 (p0) REVERT: C 107 ASP cc_start: 0.8544 (OUTLIER) cc_final: 0.8186 (p0) REVERT: C 233 MET cc_start: 0.7927 (mmp) cc_final: 0.7680 (mmm) REVERT: D 140 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7531 (mm-30) outliers start: 13 outliers final: 9 residues processed: 121 average time/residue: 0.1949 time to fit residues: 31.4441 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 210 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 24 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 79 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 48 optimal weight: 0.4980 chunk 68 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.4980 chunk 44 optimal weight: 0.6980 chunk 82 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 210 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.138095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.110877 restraints weight = 12210.842| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 2.85 r_work: 0.3336 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7017 Z= 0.188 Angle : 0.551 5.061 9447 Z= 0.294 Chirality : 0.041 0.135 1010 Planarity : 0.004 0.056 1221 Dihedral : 7.551 75.825 985 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.63 % Favored : 92.37 % Rotamer: Outliers : 2.09 % Allowed : 14.09 % Favored : 83.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.56 (0.28), residues: 839 helix: -0.54 (0.28), residues: 355 sheet: -2.46 (0.46), residues: 120 loop : -2.57 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 261 HIS 0.004 0.001 HIS B 202 PHE 0.009 0.001 PHE A 247 TYR 0.019 0.001 TYR A 37 ARG 0.003 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 107 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 206 TRP cc_start: 0.4491 (OUTLIER) cc_final: 0.3959 (m100) REVERT: A 228 ASP cc_start: 0.8313 (p0) cc_final: 0.7479 (p0) REVERT: A 229 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8505 (mmmt) REVERT: C 89 ASN cc_start: 0.8141 (p0) cc_final: 0.7833 (p0) REVERT: C 98 GLU cc_start: 0.8075 (tp30) cc_final: 0.7530 (tp30) REVERT: C 107 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8077 (p0) REVERT: C 262 ILE cc_start: 0.8240 (mp) cc_final: 0.7731 (mm) REVERT: D 140 GLU cc_start: 0.7761 (mm-30) cc_final: 0.7515 (mm-30) outliers start: 15 outliers final: 11 residues processed: 115 average time/residue: 0.1822 time to fit residues: 28.3215 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 103 time to evaluate : 0.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 6 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 3.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 121 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.137463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.108808 restraints weight = 12537.171| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.15 r_work: 0.3347 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 7017 Z= 0.240 Angle : 0.566 7.006 9447 Z= 0.298 Chirality : 0.042 0.131 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.541 72.664 985 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.65 % Allowed : 13.95 % Favored : 83.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.29), residues: 839 helix: -0.60 (0.27), residues: 368 sheet: -2.51 (0.46), residues: 122 loop : -2.52 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.010 0.001 PHE A 78 TYR 0.020 0.001 TYR A 37 ARG 0.002 0.000 ARG B 330 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.828 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8353 (p0) cc_final: 0.8107 (p0) REVERT: A 229 LYS cc_start: 0.9052 (mmmt) cc_final: 0.8597 (pttt) REVERT: A 247 PHE cc_start: 0.6040 (t80) cc_final: 0.5814 (t80) REVERT: B 467 HIS cc_start: 0.8702 (OUTLIER) cc_final: 0.8258 (m-70) REVERT: C 89 ASN cc_start: 0.8123 (p0) cc_final: 0.7847 (p0) REVERT: C 107 ASP cc_start: 0.8580 (OUTLIER) cc_final: 0.8194 (p0) REVERT: C 233 MET cc_start: 0.7830 (mmp) cc_final: 0.7580 (mmm) REVERT: D 118 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8308 (p0) outliers start: 19 outliers final: 14 residues processed: 115 average time/residue: 0.1827 time to fit residues: 28.7993 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 121 HIS Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 206 TRP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 262 ILE Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 118 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 49 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 58 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 6.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.137597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.109146 restraints weight = 12658.555| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.10 r_work: 0.3342 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 7017 Z= 0.253 Angle : 0.571 5.765 9447 Z= 0.301 Chirality : 0.042 0.135 1010 Planarity : 0.004 0.056 1221 Dihedral : 7.589 71.855 985 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.34 % Favored : 91.66 % Rotamer: Outliers : 2.37 % Allowed : 15.62 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.29), residues: 839 helix: -0.55 (0.28), residues: 369 sheet: -2.47 (0.46), residues: 122 loop : -2.52 (0.32), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 261 HIS 0.009 0.001 HIS A 121 PHE 0.010 0.001 PHE A 78 TYR 0.020 0.001 TYR A 37 ARG 0.002 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.824 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8360 (p0) cc_final: 0.8138 (p0) REVERT: A 229 LYS cc_start: 0.9069 (mmmt) cc_final: 0.8638 (pttm) REVERT: B 302 TYR cc_start: 0.7828 (t80) cc_final: 0.7394 (t80) REVERT: B 467 HIS cc_start: 0.8699 (OUTLIER) cc_final: 0.8234 (m-70) REVERT: C 89 ASN cc_start: 0.8112 (p0) cc_final: 0.7830 (p0) REVERT: C 107 ASP cc_start: 0.8607 (OUTLIER) cc_final: 0.8225 (p0) REVERT: C 233 MET cc_start: 0.7842 (mmp) cc_final: 0.7601 (mmm) outliers start: 17 outliers final: 12 residues processed: 113 average time/residue: 0.1810 time to fit residues: 27.8368 Evaluate side-chains 116 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 118 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 7 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 72 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 31 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 HIS ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.134624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.108472 restraints weight = 12527.377| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.72 r_work: 0.3304 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8237 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 7017 Z= 0.364 Angle : 0.638 7.975 9447 Z= 0.335 Chirality : 0.044 0.138 1010 Planarity : 0.005 0.057 1221 Dihedral : 8.168 78.658 985 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.93 % Allowed : 16.60 % Favored : 80.47 % 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: -2.70 (0.29), residues: 839 helix: -0.71 (0.27), residues: 369 sheet: -2.66 (0.46), residues: 123 loop : -2.58 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 261 HIS 0.007 0.001 HIS B 202 PHE 0.017 0.002 PHE A 247 TYR 0.025 0.002 TYR A 37 ARG 0.004 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 106 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8364 (p0) cc_final: 0.8140 (p0) REVERT: A 229 LYS cc_start: 0.9128 (mmmt) cc_final: 0.8640 (pttt) REVERT: B 302 TYR cc_start: 0.7847 (t80) cc_final: 0.7400 (t80) REVERT: B 467 HIS cc_start: 0.8810 (OUTLIER) cc_final: 0.8242 (m-70) REVERT: C 89 ASN cc_start: 0.8075 (p0) cc_final: 0.7813 (p0) REVERT: C 107 ASP cc_start: 0.8665 (OUTLIER) cc_final: 0.8381 (p0) REVERT: C 233 MET cc_start: 0.7890 (mmp) cc_final: 0.7655 (mmm) REVERT: C 236 LEU cc_start: 0.8329 (OUTLIER) cc_final: 0.7934 (mp) REVERT: C 262 ILE cc_start: 0.8234 (mp) cc_final: 0.7765 (mm) outliers start: 21 outliers final: 14 residues processed: 119 average time/residue: 0.1889 time to fit residues: 29.9718 Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain C residue 236 LEU Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 8 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.136931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.108650 restraints weight = 12506.486| |-----------------------------------------------------------------------------| r_work (start): 0.3501 rms_B_bonded: 3.08 r_work: 0.3346 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7017 Z= 0.220 Angle : 0.578 7.565 9447 Z= 0.305 Chirality : 0.042 0.134 1010 Planarity : 0.004 0.057 1221 Dihedral : 7.757 75.037 985 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.37 % Allowed : 17.85 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.49 (0.29), residues: 839 helix: -0.54 (0.27), residues: 375 sheet: -2.47 (0.46), residues: 122 loop : -2.55 (0.32), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.019 0.001 PHE A 247 TYR 0.021 0.001 TYR A 37 ARG 0.003 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 106 time to evaluate : 0.719 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 228 ASP cc_start: 0.8325 (p0) cc_final: 0.8111 (p0) REVERT: A 229 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8684 (pttm) REVERT: B 302 TYR cc_start: 0.7796 (t80) cc_final: 0.7365 (t80) REVERT: B 467 HIS cc_start: 0.8759 (OUTLIER) cc_final: 0.8319 (m-70) REVERT: C 89 ASN cc_start: 0.8069 (p0) cc_final: 0.7815 (p0) REVERT: C 262 ILE cc_start: 0.8172 (mp) cc_final: 0.7718 (mm) REVERT: C 271 LYS cc_start: 0.8141 (mttt) cc_final: 0.7940 (mttm) outliers start: 17 outliers final: 14 residues processed: 116 average time/residue: 0.1940 time to fit residues: 29.9194 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 102 time to evaluate : 0.740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 89 PHE Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 57 optimal weight: 1.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 24 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 20 optimal weight: 0.5980 chunk 46 optimal weight: 5.9990 chunk 2 optimal weight: 0.2980 chunk 3 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.136548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.108699 restraints weight = 12416.035| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 2.94 r_work: 0.3343 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.2279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7017 Z= 0.232 Angle : 0.620 11.360 9447 Z= 0.323 Chirality : 0.042 0.138 1010 Planarity : 0.004 0.054 1221 Dihedral : 7.654 75.972 985 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 2.51 % Allowed : 17.85 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.29), residues: 839 helix: -0.51 (0.27), residues: 375 sheet: -2.40 (0.47), residues: 122 loop : -2.53 (0.33), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 261 HIS 0.005 0.001 HIS B 202 PHE 0.017 0.001 PHE A 247 TYR 0.019 0.001 TYR A 37 ARG 0.004 0.000 ARG D 106 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.9109 (mmmt) cc_final: 0.8612 (pttt) REVERT: B 302 TYR cc_start: 0.7893 (t80) cc_final: 0.7438 (t80) REVERT: B 467 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8323 (m-70) REVERT: C 89 ASN cc_start: 0.8057 (p0) cc_final: 0.7795 (p0) REVERT: C 262 ILE cc_start: 0.8190 (mp) cc_final: 0.7739 (mm) REVERT: C 271 LYS cc_start: 0.8170 (mttt) cc_final: 0.7969 (mttm) outliers start: 18 outliers final: 15 residues processed: 114 average time/residue: 0.1953 time to fit residues: 29.8519 Evaluate side-chains 117 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 101 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 69 VAL Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain B residue 470 ASP Chi-restraints excluded: chain C residue 43 GLU Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 60 optimal weight: 0.4980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 51 optimal weight: 0.4980 chunk 9 optimal weight: 0.0670 chunk 72 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 chunk 34 optimal weight: 0.9980 chunk 1 optimal weight: 3.9990 chunk 82 optimal weight: 5.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.138222 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.109979 restraints weight = 12628.995| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.01 r_work: 0.3364 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7017 Z= 0.188 Angle : 0.603 12.567 9447 Z= 0.315 Chirality : 0.042 0.182 1010 Planarity : 0.004 0.057 1221 Dihedral : 7.400 74.073 985 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 1.81 % Allowed : 18.55 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.29), residues: 839 helix: -0.34 (0.28), residues: 371 sheet: -2.28 (0.48), residues: 122 loop : -2.48 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 214 HIS 0.004 0.001 HIS B 202 PHE 0.016 0.001 PHE A 247 TYR 0.017 0.001 TYR A 37 ARG 0.004 0.000 ARG D 106 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1678 Ramachandran restraints generated. 839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 102 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 229 LYS cc_start: 0.8827 (mmmt) cc_final: 0.8453 (mtmt) REVERT: B 302 TYR cc_start: 0.7888 (t80) cc_final: 0.7434 (t80) REVERT: B 467 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8454 (m-70) REVERT: C 89 ASN cc_start: 0.8050 (p0) cc_final: 0.7794 (p0) REVERT: C 107 ASP cc_start: 0.8644 (OUTLIER) cc_final: 0.8355 (p0) outliers start: 13 outliers final: 11 residues processed: 110 average time/residue: 0.1889 time to fit residues: 27.9081 Evaluate side-chains 111 residues out of total 717 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 98 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 62 THR Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 128 PHE Chi-restraints excluded: chain A residue 139 ILE Chi-restraints excluded: chain A residue 192 ASP Chi-restraints excluded: chain A residue 207 ARG Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 467 HIS Chi-restraints excluded: chain C residue 91 LEU Chi-restraints excluded: chain C residue 107 ASP Chi-restraints excluded: chain D residue 141 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 85 random chunks: chunk 40 optimal weight: 0.0060 chunk 6 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 65 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 10 optimal weight: 0.0970 chunk 83 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.137612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.110574 restraints weight = 12272.526| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 2.80 r_work: 0.3369 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7017 Z= 0.196 Angle : 0.599 12.773 9447 Z= 0.312 Chirality : 0.041 0.156 1010 Planarity : 0.004 0.055 1221 Dihedral : 7.358 73.259 985 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.10 % Favored : 91.90 % Rotamer: Outliers : 2.09 % Allowed : 18.13 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.22 (0.30), residues: 839 helix: -0.31 (0.28), residues: 373 sheet: -2.21 (0.49), residues: 122 loop : -2.45 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 214 HIS 0.004 0.001 HIS B 202 PHE 0.020 0.001 PHE B 233 TYR 0.016 0.001 TYR A 37 ARG 0.003 0.000 ARG D 106 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3118.85 seconds wall clock time: 54 minutes 27.44 seconds (3267.44 seconds total)