Starting phenix.real_space_refine on Thu Jul 2 06:05:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i28_52579/07_2026/9i28_52579.map" } resolution = 2.93 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= 0.000 sd= 1.700 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: 6 Type Number sf(0) Gaussians P 4 5.49 5 Mg 2 5.21 5 S 36 5.16 5 C 4354 2.51 5 N 1198 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6908 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 427} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 3432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3432 Classifications: {'peptide': 449} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 427} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {' MG': 1, 'CAP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.80, per 1000 atoms: 0.26 Number of scatterers: 6908 At special positions: 0 Unit cell: (112.005, 83.185, 65.5, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 36 16.00 P 4 15.00 Mg 2 11.99 O 1314 8.00 N 1198 7.00 C 4354 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=0, symmetry=0 Time building additional restraints: 0.49 Conformation dependent library (CDL) restraints added in 272.4 milliseconds 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 6 sheets defined 48.8% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 13 through 21 Processing helix chain 'A' and resid 37 through 50 Processing helix chain 'A' and resid 61 through 67 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'A' and resid 100 through 110 removed outlier: 3.720A pdb=" N PHE A 104 " --> pdb=" O MET A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 134 Processing helix chain 'A' and resid 142 through 151 removed outlier: 3.886A pdb=" N LEU A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 184 Processing helix chain 'A' and resid 203 through 223 Processing helix chain 'A' and resid 236 through 252 Processing helix chain 'A' and resid 253 through 256 removed outlier: 4.632A pdb=" N SER A 256 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 253 through 256' Processing helix chain 'A' and resid 267 through 279 removed outlier: 4.079A pdb=" N ALA A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE A 272 " --> pdb=" O GLY A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.719A pdb=" N SER A 296 " --> pdb=" O GLY A 292 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 316 Processing helix chain 'A' and resid 333 through 335 No H-bonds generated for 'chain 'A' and resid 333 through 335' Processing helix chain 'A' and resid 336 through 345 removed outlier: 3.697A pdb=" N ALA A 340 " --> pdb=" O ASP A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 375 through 384 Processing helix chain 'A' and resid 402 through 419 Processing helix chain 'A' and resid 422 through 430 removed outlier: 3.718A pdb=" N GLU A 429 " --> pdb=" O ASP A 425 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 440 removed outlier: 3.517A pdb=" N PHE A 437 " --> pdb=" O LEU A 433 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLU A 438 " --> pdb=" O ALA A 434 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N PHE A 440 " --> pdb=" O ALA A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 448 Processing helix chain 'B' and resid 13 through 21 Processing helix chain 'B' and resid 37 through 50 Processing helix chain 'B' and resid 61 through 67 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'B' and resid 100 through 110 removed outlier: 3.724A pdb=" N PHE B 104 " --> pdb=" O MET B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 114 Processing helix chain 'B' and resid 129 through 134 Processing helix chain 'B' and resid 142 through 151 removed outlier: 3.886A pdb=" N LEU B 146 " --> pdb=" O ASN B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 172 through 184 Processing helix chain 'B' and resid 203 through 223 Processing helix chain 'B' and resid 236 through 252 removed outlier: 3.554A pdb=" N GLY B 252 " --> pdb=" O LEU B 248 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 256 removed outlier: 4.569A pdb=" N SER B 256 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 253 through 256' Processing helix chain 'B' and resid 267 through 279 removed outlier: 4.053A pdb=" N ALA B 271 " --> pdb=" O ALA B 267 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 removed outlier: 3.720A pdb=" N SER B 296 " --> pdb=" O GLY B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 316 Processing helix chain 'B' and resid 333 through 335 No H-bonds generated for 'chain 'B' and resid 333 through 335' Processing helix chain 'B' and resid 336 through 345 removed outlier: 3.700A pdb=" N ALA B 340 " --> pdb=" O ASP B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 375 through 384 Processing helix chain 'B' and resid 402 through 419 Processing helix chain 'B' and resid 422 through 430 removed outlier: 3.684A pdb=" N GLU B 429 " --> pdb=" O ASP B 425 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 440 removed outlier: 3.517A pdb=" N PHE B 440 " --> pdb=" O ALA B 436 " (cutoff:3.500A) Processing helix chain 'B' and resid 440 through 448 Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 75 removed outlier: 6.666A pdb=" N LYS A 82 " --> pdb=" O TYR A 72 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N VAL A 74 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N LEU A 80 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 25 " --> pdb=" O PHE A 126 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N PHE A 126 " --> pdb=" O LEU A 25 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA A 27 " --> pdb=" O HIS A 124 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY A 302 " --> pdb=" O ALA A 121 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 164 removed outlier: 6.966A pdb=" N ILE A 190 " --> pdb=" O SER A 229 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ASN A 231 " --> pdb=" O ILE A 190 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N PHE A 228 " --> pdb=" O ALA A 259 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU A 261 " --> pdb=" O PHE A 228 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ALA A 230 " --> pdb=" O LEU A 261 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N THR A 391 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N ILE A 367 " --> pdb=" O THR A 391 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 347 through 349 Processing sheet with id=AA4, first strand: chain 'B' and resid 70 through 75 removed outlier: 6.655A pdb=" N LYS B 82 " --> pdb=" O TYR B 72 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N VAL B 74 " --> pdb=" O LEU B 80 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU B 80 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU B 25 " --> pdb=" O PHE B 126 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N PHE B 126 " --> pdb=" O LEU B 25 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ALA B 27 " --> pdb=" O HIS B 124 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N GLY B 302 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 160 through 164 removed outlier: 6.747A pdb=" N VAL B 161 " --> pdb=" O PHE B 189 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N KCX B 191 " --> pdb=" O VAL B 161 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N THR B 163 " --> pdb=" O KCX B 191 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE B 190 " --> pdb=" O SER B 229 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N ASN B 231 " --> pdb=" O ILE B 190 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N PHE B 228 " --> pdb=" O ALA B 259 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU B 261 " --> pdb=" O PHE B 228 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 230 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 320 " --> pdb=" O ILE B 366 " (cutoff:3.500A) removed outlier: 7.413A pdb=" N THR B 391 " --> pdb=" O PRO B 365 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE B 367 " --> pdb=" O THR B 391 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 347 through 349 305 hydrogen bonds defined for protein. 897 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: 0.92 Time building geometry restraints manager: 0.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1285 1.32 - 1.45: 1860 1.45 - 1.57: 3861 1.57 - 1.69: 4 1.69 - 1.81: 62 Bond restraints: 7072 Sorted by residual: bond pdb=" O5 CAP B 501 " pdb=" P2 CAP B 501 " ideal model delta sigma weight residual 1.700 1.587 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" O5 CAP A 501 " pdb=" P2 CAP A 501 " ideal model delta sigma weight residual 1.700 1.587 0.113 2.00e-02 2.50e+03 3.18e+01 bond pdb=" O1 CAP A 501 " pdb=" P1 CAP A 501 " ideal model delta sigma weight residual 1.708 1.596 0.112 2.00e-02 2.50e+03 3.15e+01 bond pdb=" O1 CAP B 501 " pdb=" P1 CAP B 501 " ideal model delta sigma weight residual 1.708 1.597 0.111 2.00e-02 2.50e+03 3.09e+01 bond pdb=" NZ KCX A 191 " pdb=" CX KCX A 191 " ideal model delta sigma weight residual 1.411 1.329 0.082 2.00e-02 2.50e+03 1.69e+01 ... (remaining 7067 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.41: 9303 1.41 - 2.82: 224 2.82 - 4.23: 46 4.23 - 5.64: 9 5.64 - 7.05: 12 Bond angle restraints: 9594 Sorted by residual: angle pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" N GLN B 196 " ideal model delta sigma weight residual 116.45 119.52 -3.07 8.50e-01 1.38e+00 1.30e+01 angle pdb=" CA PRO B 195 " pdb=" C PRO B 195 " pdb=" O PRO B 195 " ideal model delta sigma weight residual 121.38 118.76 2.62 7.70e-01 1.69e+00 1.15e+01 angle pdb=" CA ASP A 117 " pdb=" CB ASP A 117 " pdb=" CG ASP A 117 " ideal model delta sigma weight residual 112.60 115.51 -2.91 1.00e+00 1.00e+00 8.47e+00 angle pdb=" CA ASP B 117 " pdb=" CB ASP B 117 " pdb=" CG ASP B 117 " ideal model delta sigma weight residual 112.60 115.47 -2.87 1.00e+00 1.00e+00 8.23e+00 angle pdb=" C GLU B 194 " pdb=" N PRO B 195 " pdb=" CA PRO B 195 " ideal model delta sigma weight residual 121.65 118.95 2.70 1.01e+00 9.80e-01 7.15e+00 ... (remaining 9589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.45: 3762 15.45 - 30.91: 308 30.91 - 46.36: 75 46.36 - 61.82: 21 61.82 - 77.27: 4 Dihedral angle restraints: 4170 sinusoidal: 1640 harmonic: 2530 Sorted by residual: dihedral pdb=" CA TYR A 28 " pdb=" C TYR A 28 " pdb=" N ILE A 29 " pdb=" CA ILE A 29 " ideal model delta harmonic sigma weight residual 180.00 160.60 19.40 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA TYR B 28 " pdb=" C TYR B 28 " pdb=" N ILE B 29 " pdb=" CA ILE B 29 " ideal model delta harmonic sigma weight residual 180.00 160.62 19.38 0 5.00e+00 4.00e-02 1.50e+01 dihedral pdb=" CA ASP A 68 " pdb=" C ASP A 68 " pdb=" N ALA A 69 " pdb=" CA ALA A 69 " ideal model delta harmonic sigma weight residual 180.00 165.28 14.72 0 5.00e+00 4.00e-02 8.66e+00 ... (remaining 4167 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 907 0.069 - 0.137: 100 0.137 - 0.205: 1 0.205 - 0.274: 0 0.274 - 0.342: 4 Chirality restraints: 1012 Sorted by residual: chirality pdb=" C2 CAP B 501 " pdb=" C CAP B 501 " pdb=" C3 CAP B 501 " pdb=" O2 CAP B 501 " both_signs ideal model delta sigma weight residual False -2.76 -2.42 -0.34 2.00e-01 2.50e+01 2.93e+00 chirality pdb=" C2 CAP A 501 " pdb=" C CAP A 501 " pdb=" C3 CAP A 501 " pdb=" O2 CAP A 501 " both_signs ideal model delta sigma weight residual False -2.76 -2.43 -0.33 2.00e-01 2.50e+01 2.76e+00 chirality pdb=" C3 CAP B 501 " pdb=" C2 CAP B 501 " pdb=" C4 CAP B 501 " pdb=" O3 CAP B 501 " both_signs ideal model delta sigma weight residual False -2.19 -2.50 0.30 2.00e-01 2.50e+01 2.32e+00 ... (remaining 1009 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 364 " 0.036 5.00e-02 4.00e+02 5.40e-02 4.66e+00 pdb=" N PRO A 365 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 365 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 365 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 190 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.20e+00 pdb=" C ILE B 190 " 0.035 2.00e-02 2.50e+03 pdb=" O ILE B 190 " -0.013 2.00e-02 2.50e+03 pdb=" N KCX B 191 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CAP A 501 " 0.023 2.00e-02 2.50e+03 1.33e-02 1.77e+00 pdb=" C2 CAP A 501 " -0.007 2.00e-02 2.50e+03 pdb=" O6 CAP A 501 " -0.008 2.00e-02 2.50e+03 pdb=" O7 CAP A 501 " -0.008 2.00e-02 2.50e+03 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 38 2.64 - 3.20: 6343 3.20 - 3.77: 11498 3.77 - 4.33: 17148 4.33 - 4.90: 27333 Nonbonded interactions: 62360 Sorted by model distance: nonbonded pdb="MG MG B 500 " pdb=" O6 CAP B 501 " model vdw 2.073 2.170 nonbonded pdb="MG MG A 500 " pdb=" O6 CAP A 501 " model vdw 2.121 2.170 nonbonded pdb=" OQ2 KCX A 191 " pdb="MG MG A 500 " model vdw 2.125 2.170 nonbonded pdb="MG MG A 500 " pdb=" O2 CAP A 501 " model vdw 2.141 2.170 nonbonded pdb="MG MG A 500 " pdb=" O3 CAP A 501 " model vdw 2.160 2.170 ... (remaining 62355 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 4.760 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: 0.200 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.450 Find NCS groups from input model: 0.100 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:6.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 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 : 0.006 0.113 7072 Z= 0.276 Angle : 0.594 7.049 9594 Z= 0.303 Chirality : 0.047 0.342 1012 Planarity : 0.005 0.054 1270 Dihedral : 12.668 77.272 2570 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.44 % Allowed : 6.03 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -0.19 (0.27), residues: 888 helix: 0.72 (0.25), residues: 394 sheet: -1.09 (0.44), residues: 138 loop : -0.53 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 172 TYR 0.013 0.002 TYR A 286 PHE 0.013 0.002 PHE A 45 TRP 0.004 0.001 TRP B 357 HIS 0.004 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.28 ( 7072) covalent geometry : angle 0.59379 / 0.30 ( 9594) hydrogen bonds : bond 0.13984 / 9.80 ( 305) hydrogen bonds : angle 6.84494 / 4.80 ( 897) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 159 time to evaluate : 0.258 Fit side-chains REVERT: A 107 LEU cc_start: 0.8552 (mt) cc_final: 0.8157 (mp) REVERT: A 206 ASP cc_start: 0.7156 (m-30) cc_final: 0.6946 (m-30) REVERT: A 213 ASP cc_start: 0.8012 (t70) cc_final: 0.7791 (t0) REVERT: A 432 GLU cc_start: 0.8041 (mp0) cc_final: 0.7478 (mt-10) REVERT: B 432 GLU cc_start: 0.8032 (mp0) cc_final: 0.7743 (mm-30) outliers start: 3 outliers final: 2 residues processed: 162 average time/residue: 0.5066 time to fit residues: 86.6772 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 109 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 ASP Chi-restraints excluded: chain B residue 117 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 74 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 HIS A 415 GLN ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.165614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.144269 restraints weight = 8660.801| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 1.44 r_work: 0.3629 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7072 Z= 0.232 Angle : 0.589 6.760 9594 Z= 0.310 Chirality : 0.044 0.133 1012 Planarity : 0.005 0.051 1270 Dihedral : 7.512 51.947 1052 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 3.09 % Allowed : 13.82 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: -0.02 (0.27), residues: 888 helix: 0.99 (0.25), residues: 386 sheet: -1.04 (0.44), residues: 138 loop : -0.57 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 276 TYR 0.024 0.003 TYR A 448 PHE 0.013 0.002 PHE B 45 TRP 0.005 0.001 TRP B 417 HIS 0.005 0.001 HIS B 23 Details of bonding type rmsd/Z covalent geometry : bond 0.00526 / 0.23 ( 7072) covalent geometry : angle 0.58872 / 0.31 ( 9594) hydrogen bonds : bond 0.04745 / 3.25 ( 305) hydrogen bonds : angle 5.43182 / 3.80 ( 897) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 112 time to evaluate : 0.199 Fit side-chains REVERT: A 107 LEU cc_start: 0.8556 (mt) cc_final: 0.8212 (mp) REVERT: A 375 ARG cc_start: 0.8061 (OUTLIER) cc_final: 0.7762 (mtt180) REVERT: A 425 ASP cc_start: 0.8280 (m-30) cc_final: 0.7932 (m-30) REVERT: A 432 GLU cc_start: 0.8054 (mp0) cc_final: 0.7711 (mp0) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 0.4468 time to fit residues: 58.2419 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 102 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 190 ILE Chi-restraints excluded: chain A residue 249 GLU Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 424 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 71 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 66 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 415 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.169341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.148894 restraints weight = 8548.537| |-----------------------------------------------------------------------------| r_work (start): 0.3772 rms_B_bonded: 1.38 r_work: 0.3676 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 3.68 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.1531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.142 Angle : 0.516 5.910 9594 Z= 0.271 Chirality : 0.041 0.144 1012 Planarity : 0.004 0.046 1270 Dihedral : 6.238 49.613 1048 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.94 % Allowed : 15.88 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.16 (0.28), residues: 888 helix: 1.20 (0.26), residues: 386 sheet: -0.94 (0.44), residues: 138 loop : -0.56 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.024 0.002 TYR A 448 PHE 0.010 0.002 PHE B 327 TRP 0.005 0.001 TRP B 417 HIS 0.005 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 7072) covalent geometry : angle 0.51639 / 0.27 ( 9594) hydrogen bonds : bond 0.03910 / 2.66 ( 305) hydrogen bonds : angle 5.01375 / 3.51 ( 897) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 0.255 Fit side-chains REVERT: A 13 LYS cc_start: 0.8546 (mtmm) cc_final: 0.8323 (ptpt) REVERT: A 107 LEU cc_start: 0.8524 (mt) cc_final: 0.8173 (mp) REVERT: A 375 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7649 (mtt180) REVERT: A 432 GLU cc_start: 0.7952 (mp0) cc_final: 0.7633 (mp0) REVERT: B 375 ARG cc_start: 0.8027 (OUTLIER) cc_final: 0.7728 (mtt180) outliers start: 20 outliers final: 5 residues processed: 128 average time/residue: 0.5182 time to fit residues: 70.0297 Evaluate side-chains 111 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 104 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 30 optimal weight: 0.7980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 23 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 0.3980 chunk 80 optimal weight: 10.0000 chunk 3 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 399 HIS ** 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 = 0.3987 r_free = 0.3987 target = 0.167696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146251 restraints weight = 8756.966| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 1.49 r_work: 0.3661 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3538 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 7072 Z= 0.123 Angle : 0.508 5.355 9594 Z= 0.265 Chirality : 0.041 0.142 1012 Planarity : 0.004 0.046 1270 Dihedral : 5.958 52.348 1048 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.53 % Allowed : 17.50 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.29 (0.28), residues: 888 helix: 1.32 (0.26), residues: 384 sheet: -0.87 (0.43), residues: 138 loop : -0.51 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 276 TYR 0.025 0.002 TYR B 448 PHE 0.010 0.001 PHE B 45 TRP 0.005 0.001 TRP B 417 HIS 0.004 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 ( 7072) covalent geometry : angle 0.50778 / 0.27 ( 9594) hydrogen bonds : bond 0.03583 / 2.44 ( 305) hydrogen bonds : angle 4.80702 / 3.36 ( 897) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.197 Fit side-chains REVERT: A 107 LEU cc_start: 0.8576 (mt) cc_final: 0.8222 (mp) REVERT: A 375 ARG cc_start: 0.7941 (OUTLIER) cc_final: 0.7609 (mtt180) REVERT: A 432 GLU cc_start: 0.7977 (mp0) cc_final: 0.7675 (mp0) REVERT: B 115 MET cc_start: 0.7515 (OUTLIER) cc_final: 0.7125 (mtt) REVERT: B 400 ILE cc_start: 0.8472 (tt) cc_final: 0.7862 (pt) outliers start: 24 outliers final: 7 residues processed: 131 average time/residue: 0.4858 time to fit residues: 67.1192 Evaluate side-chains 114 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 105 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 13 optimal weight: 1.9990 chunk 52 optimal weight: 0.1980 chunk 87 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 3 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 35 optimal weight: 0.5980 chunk 77 optimal weight: 0.3980 chunk 42 optimal weight: 0.5980 chunk 50 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 HIS ** 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 = 0.3999 r_free = 0.3999 target = 0.168844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.147256 restraints weight = 8788.416| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.51 r_work: 0.3673 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.116 Angle : 0.511 5.241 9594 Z= 0.267 Chirality : 0.041 0.143 1012 Planarity : 0.004 0.045 1270 Dihedral : 5.736 51.140 1048 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.24 % Allowed : 20.29 % Favored : 76.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.39 (0.28), residues: 888 helix: 1.40 (0.26), residues: 384 sheet: -0.78 (0.43), residues: 136 loop : -0.47 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.024 0.002 TYR A 448 PHE 0.010 0.001 PHE B 45 TRP 0.006 0.001 TRP B 417 HIS 0.007 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7072) covalent geometry : angle 0.51059 / 0.27 ( 9594) hydrogen bonds : bond 0.03451 / 2.34 ( 305) hydrogen bonds : angle 4.70243 / 3.28 ( 897) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.283 Fit side-chains REVERT: A 13 LYS cc_start: 0.8583 (mtmm) cc_final: 0.8345 (ptpt) REVERT: A 107 LEU cc_start: 0.8584 (mt) cc_final: 0.8215 (mp) REVERT: A 400 ILE cc_start: 0.8477 (tt) cc_final: 0.7904 (pt) REVERT: B 72 TYR cc_start: 0.8029 (p90) cc_final: 0.7653 (p90) REVERT: B 115 MET cc_start: 0.7471 (OUTLIER) cc_final: 0.7238 (mtt) REVERT: B 375 ARG cc_start: 0.7983 (OUTLIER) cc_final: 0.7688 (mtt180) REVERT: B 400 ILE cc_start: 0.8343 (tt) cc_final: 0.7942 (pt) outliers start: 22 outliers final: 8 residues processed: 126 average time/residue: 0.4292 time to fit residues: 57.2641 Evaluate side-chains 116 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 106 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 78 optimal weight: 0.0020 chunk 49 optimal weight: 0.9990 chunk 39 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 53 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 54 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 overall best weight: 0.6592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 399 HIS ** 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 = 0.3994 r_free = 0.3994 target = 0.168633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.146970 restraints weight = 8693.248| |-----------------------------------------------------------------------------| r_work (start): 0.3753 rms_B_bonded: 1.50 r_work: 0.3657 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.125 Angle : 0.526 5.363 9594 Z= 0.276 Chirality : 0.042 0.141 1012 Planarity : 0.004 0.045 1270 Dihedral : 5.760 51.661 1048 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.94 % Allowed : 20.00 % Favored : 77.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.40 (0.28), residues: 888 helix: 1.41 (0.26), residues: 384 sheet: -0.77 (0.43), residues: 136 loop : -0.45 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.023 0.002 TYR B 448 PHE 0.010 0.001 PHE B 45 TRP 0.006 0.001 TRP B 417 HIS 0.003 0.001 HIS B 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7072) covalent geometry : angle 0.52629 / 0.28 ( 9594) hydrogen bonds : bond 0.03518 / 2.40 ( 305) hydrogen bonds : angle 4.68736 / 3.28 ( 897) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 109 time to evaluate : 0.176 Fit side-chains REVERT: A 107 LEU cc_start: 0.8577 (mt) cc_final: 0.8216 (mp) REVERT: A 400 ILE cc_start: 0.8417 (tt) cc_final: 0.7868 (pt) REVERT: A 432 GLU cc_start: 0.8188 (mm-30) cc_final: 0.7783 (mm-30) REVERT: B 72 TYR cc_start: 0.7950 (p90) cc_final: 0.7558 (p90) REVERT: B 115 MET cc_start: 0.7492 (OUTLIER) cc_final: 0.7268 (mtt) REVERT: B 375 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7651 (mtt180) REVERT: B 400 ILE cc_start: 0.8395 (tt) cc_final: 0.7953 (pt) REVERT: B 432 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7898 (mm-30) outliers start: 20 outliers final: 9 residues processed: 120 average time/residue: 0.4490 time to fit residues: 57.1887 Evaluate side-chains 118 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 107 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 188 ASP Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 375 ARG Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 14 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 81 optimal weight: 0.0670 chunk 16 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 78 optimal weight: 0.0570 chunk 75 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 43 optimal weight: 8.9990 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 399 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.169488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.147807 restraints weight = 8642.870| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.50 r_work: 0.3671 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7072 Z= 0.116 Angle : 0.529 5.362 9594 Z= 0.277 Chirality : 0.042 0.150 1012 Planarity : 0.004 0.043 1270 Dihedral : 5.608 50.093 1048 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 2.79 % Allowed : 21.76 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.32 (0.28), residues: 888 helix: 1.37 (0.26), residues: 396 sheet: -1.03 (0.43), residues: 146 loop : -0.47 (0.32), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 276 TYR 0.025 0.002 TYR A 448 PHE 0.010 0.001 PHE B 45 TRP 0.006 0.001 TRP B 417 HIS 0.009 0.001 HIS B 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00262 / 0.12 ( 7072) covalent geometry : angle 0.52869 / 0.28 ( 9594) hydrogen bonds : bond 0.03385 / 2.31 ( 305) hydrogen bonds : angle 4.63919 / 3.25 ( 897) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 116 time to evaluate : 0.185 Fit side-chains REVERT: A 103 SER cc_start: 0.8844 (t) cc_final: 0.8260 (m) REVERT: A 107 LEU cc_start: 0.8562 (mt) cc_final: 0.8233 (mp) REVERT: A 400 ILE cc_start: 0.8335 (tt) cc_final: 0.8023 (pt) REVERT: A 432 GLU cc_start: 0.8167 (mm-30) cc_final: 0.7737 (mm-30) REVERT: B 72 TYR cc_start: 0.7937 (p90) cc_final: 0.7573 (p90) REVERT: B 115 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7272 (mtt) REVERT: B 400 ILE cc_start: 0.8329 (tt) cc_final: 0.7902 (pt) REVERT: B 432 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7876 (mm-30) outliers start: 19 outliers final: 10 residues processed: 125 average time/residue: 0.5275 time to fit residues: 69.7926 Evaluate side-chains 120 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 109 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 chunk 55 optimal weight: 6.9990 chunk 66 optimal weight: 5.9990 chunk 3 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 86 optimal weight: 5.9990 chunk 80 optimal weight: 5.9990 chunk 46 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 399 HIS ** 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 = 0.3959 r_free = 0.3959 target = 0.165113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.143194 restraints weight = 8766.625| |-----------------------------------------------------------------------------| r_work (start): 0.3715 rms_B_bonded: 1.49 r_work: 0.3624 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3502 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7072 Z= 0.190 Angle : 0.590 6.226 9594 Z= 0.311 Chirality : 0.044 0.136 1012 Planarity : 0.004 0.043 1270 Dihedral : 6.288 52.266 1048 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.21 % Allowed : 23.38 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.18 (0.27), residues: 888 helix: 1.23 (0.26), residues: 380 sheet: -1.06 (0.43), residues: 146 loop : -0.46 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 78 TYR 0.027 0.002 TYR B 448 PHE 0.013 0.002 PHE B 45 TRP 0.004 0.001 TRP B 417 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.19 ( 7072) covalent geometry : angle 0.58999 / 0.31 ( 9594) hydrogen bonds : bond 0.03964 / 2.73 ( 305) hydrogen bonds : angle 4.86930 / 3.42 ( 897) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 111 time to evaluate : 0.211 Fit side-chains REVERT: A 103 SER cc_start: 0.8883 (t) cc_final: 0.8294 (m) REVERT: A 107 LEU cc_start: 0.8613 (mt) cc_final: 0.8278 (mp) REVERT: A 400 ILE cc_start: 0.8561 (tt) cc_final: 0.7860 (pt) REVERT: B 72 TYR cc_start: 0.7966 (p90) cc_final: 0.7618 (p90) REVERT: B 115 MET cc_start: 0.7575 (OUTLIER) cc_final: 0.7225 (mtt) REVERT: B 123 MET cc_start: 0.8625 (ttp) cc_final: 0.8351 (ttp) REVERT: B 400 ILE cc_start: 0.8389 (tt) cc_final: 0.7970 (pt) REVERT: B 432 GLU cc_start: 0.8286 (mm-30) cc_final: 0.8003 (mm-30) outliers start: 15 outliers final: 8 residues processed: 120 average time/residue: 0.4555 time to fit residues: 57.9368 Evaluate side-chains 113 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 0.5980 chunk 5 optimal weight: 9.9990 chunk 7 optimal weight: 0.5980 chunk 71 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 80 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 chunk 87 optimal weight: 0.0370 chunk 79 optimal weight: 1.9990 overall best weight: 0.5858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 399 HIS B 415 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.169135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.147212 restraints weight = 8720.988| |-----------------------------------------------------------------------------| r_work (start): 0.3768 rms_B_bonded: 1.52 r_work: 0.3673 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3550 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.121 Angle : 0.546 7.118 9594 Z= 0.284 Chirality : 0.042 0.148 1012 Planarity : 0.004 0.041 1270 Dihedral : 5.656 47.708 1048 Min Nonbonded Distance : 1.931 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.79 % Allowed : 23.09 % Favored : 74.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.27 (0.28), residues: 888 helix: 1.28 (0.26), residues: 392 sheet: -1.02 (0.43), residues: 146 loop : -0.42 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 78 TYR 0.021 0.002 TYR A 448 PHE 0.010 0.001 PHE B 45 TRP 0.006 0.001 TRP A 184 HIS 0.012 0.001 HIS A 399 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 7072) covalent geometry : angle 0.54598 / 0.28 ( 9594) hydrogen bonds : bond 0.03459 / 2.34 ( 305) hydrogen bonds : angle 4.73034 / 3.32 ( 897) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 112 time to evaluate : 0.265 Fit side-chains REVERT: A 107 LEU cc_start: 0.8624 (mt) cc_final: 0.8249 (mp) REVERT: A 375 ARG cc_start: 0.7905 (OUTLIER) cc_final: 0.7543 (mtt180) REVERT: A 400 ILE cc_start: 0.8512 (tt) cc_final: 0.7813 (pt) REVERT: A 432 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 72 TYR cc_start: 0.7932 (p90) cc_final: 0.7607 (p90) REVERT: B 115 MET cc_start: 0.7503 (OUTLIER) cc_final: 0.7258 (mtt) REVERT: B 123 MET cc_start: 0.8585 (ttp) cc_final: 0.8326 (ttp) REVERT: B 400 ILE cc_start: 0.8327 (tt) cc_final: 0.8020 (pt) REVERT: B 432 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7869 (mm-30) outliers start: 19 outliers final: 10 residues processed: 123 average time/residue: 0.4943 time to fit residues: 64.4525 Evaluate side-chains 121 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 109 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 375 ARG Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 28 optimal weight: 3.9990 chunk 66 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 53 optimal weight: 0.0980 chunk 47 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 73 optimal weight: 0.6980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.168642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.146759 restraints weight = 8675.898| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.50 r_work: 0.3666 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7072 Z= 0.131 Angle : 0.560 9.625 9594 Z= 0.291 Chirality : 0.042 0.145 1012 Planarity : 0.004 0.038 1270 Dihedral : 5.788 48.987 1048 Min Nonbonded Distance : 1.927 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 2.21 % Allowed : 23.38 % Favored : 74.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.18 (0.28), residues: 888 helix: 1.04 (0.25), residues: 404 sheet: -1.00 (0.43), residues: 146 loop : -0.34 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 78 TYR 0.025 0.002 TYR B 448 PHE 0.010 0.001 PHE B 45 TRP 0.020 0.001 TRP A 184 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 ( 7072) covalent geometry : angle 0.56014 / 0.29 ( 9594) hydrogen bonds : bond 0.03543 / 2.42 ( 305) hydrogen bonds : angle 4.74773 / 3.33 ( 897) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1776 Ramachandran restraints generated. 888 Oldfield, 0 Emsley, 888 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 112 time to evaluate : 0.288 Fit side-chains REVERT: A 103 SER cc_start: 0.8753 (t) cc_final: 0.8230 (m) REVERT: A 107 LEU cc_start: 0.8602 (mt) cc_final: 0.8263 (mp) REVERT: A 400 ILE cc_start: 0.8348 (tt) cc_final: 0.7661 (pt) REVERT: A 432 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7757 (mm-30) REVERT: B 72 TYR cc_start: 0.7921 (p90) cc_final: 0.7605 (p90) REVERT: B 115 MET cc_start: 0.7501 (OUTLIER) cc_final: 0.7286 (mtt) REVERT: B 123 MET cc_start: 0.8582 (ttp) cc_final: 0.8322 (ttp) REVERT: B 400 ILE cc_start: 0.8376 (tt) cc_final: 0.7879 (pt) REVERT: B 432 GLU cc_start: 0.8172 (mm-30) cc_final: 0.7870 (mm-30) outliers start: 15 outliers final: 11 residues processed: 122 average time/residue: 0.5029 time to fit residues: 64.8705 Evaluate side-chains 122 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 110 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 THR Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 194 GLU Chi-restraints excluded: chain A residue 213 ASP Chi-restraints excluded: chain A residue 334 SER Chi-restraints excluded: chain A residue 404 VAL Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 115 MET Chi-restraints excluded: chain B residue 188 ASP Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 213 ASP Chi-restraints excluded: chain B residue 404 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 85 optimal weight: 0.8980 chunk 54 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 68 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.170320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.148183 restraints weight = 8677.441| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 1.54 r_work: 0.3668 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3545 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7072 Z= 0.130 Angle : 0.566 11.444 9594 Z= 0.292 Chirality : 0.042 0.145 1012 Planarity : 0.004 0.037 1270 Dihedral : 5.725 48.496 1048 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.76 % Allowed : 23.53 % Favored : 74.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 are not related in a simple way. whole: 0.18 (0.28), residues: 888 helix: 1.03 (0.25), residues: 404 sheet: -0.99 (0.43), residues: 146 loop : -0.33 (0.33), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 301 TYR 0.018 0.002 TYR B 448 PHE 0.011 0.001 PHE B 45 TRP 0.030 0.001 TRP A 184 HIS 0.005 0.001 HIS A 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 ( 7072) covalent geometry : angle 0.56647 / 0.29 ( 9594) hydrogen bonds : bond 0.03505 / 2.37 ( 305) hydrogen bonds : angle 4.73216 / 3.33 ( 897) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2290.43 seconds wall clock time: 39 minutes 51.00 seconds (2391.00 seconds total)