Starting phenix.real_space_refine on Sun Jul 27 09:30:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.cif Found real_map, /net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.87 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.map" model { file = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7p02_13141/07_2025/7p02_13141.cif" } resolution = 2.87 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= -0.001 sd= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 63 5.16 5 C 5805 2.51 5 N 1542 2.21 5 O 1652 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9062 Number of models: 1 Model: "" Number of chains: 8 Chain: "H" Number of atoms: 1785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1785 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "B" Number of atoms: 2559 Number of conformers: 1 Conformer: "" Number of residues, atoms: 333, 2559 Classifications: {'peptide': 333} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 327} Chain: "G" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 396 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 4, 'TRANS': 46} Chain: "A" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1870 Classifications: {'peptide': 226} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 219} Chain breaks: 1 Chain: "R" Number of atoms: 2347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2347 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 13, 'TRANS': 273} Chain breaks: 1 Chain: "P" Number of atoms: 76 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 76 Classifications: {'peptide': 9} Link IDs: {'PTRANS': 1, 'TRANS': 7} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.87, per 1000 atoms: 0.76 Number of scatterers: 9062 At special positions: 0 Unit cell: (88.536, 123.69, 130.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 63 16.00 O 1652 8.00 N 1542 7.00 C 5805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 39 " - pdb=" SG CYS H 113 " distance=2.03 Simple disulfide: pdb=" SG CYS H 176 " - pdb=" SG CYS H 246 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 180 " distance=2.04 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: 2.62 Conformation dependent library (CDL) restraints added in 1.1 seconds 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2144 Finding SS restraints... Secondary structure from input PDB file: 32 helices and 14 sheets defined 39.5% alpha, 21.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'H' and resid 45 through 49 Processing helix chain 'H' and resid 79 through 82 Processing helix chain 'H' and resid 104 through 108 removed outlier: 3.645A pdb=" N THR H 108 " --> pdb=" O SER H 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 9 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'B' and resid 85 through 87 No H-bonds generated for 'chain 'B' and resid 85 through 87' Processing helix chain 'G' and resid 13 through 25 Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'A' and resid 6 through 33 Processing helix chain 'A' and resid 45 through 49 removed outlier: 3.539A pdb=" N ILE A 49 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 246 through 262 removed outlier: 3.709A pdb=" N GLN A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N GLU A 251 " --> pdb=" O ASN A 247 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 266 removed outlier: 3.707A pdb=" N ARG A 266 " --> pdb=" O ARG A 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 266' Processing helix chain 'A' and resid 276 through 287 Processing helix chain 'A' and resid 290 through 295 removed outlier: 3.762A pdb=" N TYR A 294 " --> pdb=" O LYS A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 301 removed outlier: 4.350A pdb=" N ARG A 300 " --> pdb=" O PRO A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 335 removed outlier: 4.001A pdb=" N SER A 335 " --> pdb=" O ILE A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 374 Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 66 through 84 removed outlier: 4.421A pdb=" N PHE R 70 " --> pdb=" O VAL R 66 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N LEU R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 4.272A pdb=" N HIS R 95 " --> pdb=" O THR R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 109 Processing helix chain 'R' and resid 110 through 136 Processing helix chain 'R' and resid 143 through 168 Proline residue: R 164 - end of helix Processing helix chain 'R' and resid 190 through 205 removed outlier: 3.536A pdb=" N HIS R 197 " --> pdb=" O GLU R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 205 through 225 Processing helix chain 'R' and resid 238 through 274 Proline residue: R 263 - end of helix Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 274 through 279 removed outlier: 4.158A pdb=" N TYR R 278 " --> pdb=" O ASN R 274 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 296 removed outlier: 4.165A pdb=" N GLN R 285 " --> pdb=" O LYS R 281 " (cutoff:3.500A) Processing helix chain 'R' and resid 296 through 309 removed outlier: 3.611A pdb=" N TYR R 300 " --> pdb=" O SER R 296 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ASN R 301 " --> pdb=" O SER R 297 " (cutoff:3.500A) Proline residue: R 302 - end of helix Processing helix chain 'R' and resid 309 through 319 removed outlier: 3.859A pdb=" N ARG R 313 " --> pdb=" O ASN R 309 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 20 through 24 Processing sheet with id=AA2, first strand: chain 'H' and resid 27 through 29 removed outlier: 6.765A pdb=" N MET H 51 " --> pdb=" O TYR H 67 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TYR H 67 " --> pdb=" O MET H 51 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N TRP H 53 " --> pdb=" O VAL H 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AA4, first strand: chain 'H' and resid 163 through 165 removed outlier: 6.158A pdb=" N LEU H 195 " --> pdb=" O LEU H 204 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N LEU H 204 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 46 through 52 removed outlier: 5.452A pdb=" N THR B 47 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N ASN B 340 " --> pdb=" O THR B 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.753A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 100 through 105 removed outlier: 5.909A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.548A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.155A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 229 through 234 removed outlier: 3.562A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.248A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.104A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 34 through 37 Processing sheet with id=AB4, first strand: chain 'A' and resid 39 through 40 removed outlier: 7.154A pdb=" N LEU A 39 " --> pdb=" O VAL A 240 " (cutoff:3.500A) removed outlier: 9.166A pdb=" N ASP A 242 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N PHE A 239 " --> pdb=" O PHE A 273 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ASN A 275 " --> pdb=" O PHE A 239 " (cutoff:3.500A) removed outlier: 6.040A pdb=" N VAL A 241 " --> pdb=" O ASN A 275 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'R' and resid 169 through 173 461 hydrogen bonds defined for protein. 1311 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.76 Time building geometry restraints manager: 3.05 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: 1689 1.32 - 1.45: 2402 1.45 - 1.57: 5094 1.57 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 9279 Sorted by residual: bond pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 1.332 1.439 -0.107 1.36e-02 5.41e+03 6.14e+01 bond pdb=" CG ASN R 96 " pdb=" OD1 ASN R 96 " ideal model delta sigma weight residual 1.231 1.323 -0.092 1.90e-02 2.77e+03 2.35e+01 bond pdb=" N PHE R 111 " pdb=" CA PHE R 111 " ideal model delta sigma weight residual 1.463 1.497 -0.033 6.90e-03 2.10e+04 2.34e+01 bond pdb=" CG ASN R 96 " pdb=" ND2 ASN R 96 " ideal model delta sigma weight residual 1.328 1.229 0.099 2.10e-02 2.27e+03 2.24e+01 bond pdb=" C CYS B 103 " pdb=" N ALA B 104 " ideal model delta sigma weight residual 1.330 1.268 0.061 1.41e-02 5.03e+03 1.90e+01 ... (remaining 9274 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.01: 10070 2.01 - 4.02: 2426 4.02 - 6.03: 90 6.03 - 8.05: 7 8.05 - 10.06: 3 Bond angle restraints: 12596 Sorted by residual: angle pdb=" CA VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 116.33 125.15 -8.82 1.03e+00 9.43e-01 7.33e+01 angle pdb=" N ASP B 154 " pdb=" CA ASP B 154 " pdb=" C ASP B 154 " ideal model delta sigma weight residual 113.02 103.88 9.14 1.20e+00 6.94e-01 5.81e+01 angle pdb=" C HIS B 311 " pdb=" N ASP B 312 " pdb=" CA ASP B 312 " ideal model delta sigma weight residual 122.60 112.54 10.06 1.56e+00 4.11e-01 4.16e+01 angle pdb=" O VAL B 187 " pdb=" C VAL B 187 " pdb=" N MET B 188 " ideal model delta sigma weight residual 122.66 116.62 6.04 1.07e+00 8.73e-01 3.19e+01 angle pdb=" N LEU B 152 " pdb=" CA LEU B 152 " pdb=" C LEU B 152 " ideal model delta sigma weight residual 112.68 105.34 7.34 1.33e+00 5.65e-01 3.04e+01 ... (remaining 12591 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.70: 5129 16.70 - 33.39: 309 33.39 - 50.09: 64 50.09 - 66.79: 21 66.79 - 83.48: 3 Dihedral angle restraints: 5526 sinusoidal: 2202 harmonic: 3324 Sorted by residual: dihedral pdb=" CB CYS H 39 " pdb=" SG CYS H 39 " pdb=" SG CYS H 113 " pdb=" CB CYS H 113 " ideal model delta sinusoidal sigma weight residual 93.00 60.66 32.34 1 1.00e+01 1.00e-02 1.49e+01 dihedral pdb=" C PHE B 151 " pdb=" N PHE B 151 " pdb=" CA PHE B 151 " pdb=" CB PHE B 151 " ideal model delta harmonic sigma weight residual -122.60 -113.69 -8.91 0 2.50e+00 1.60e-01 1.27e+01 dihedral pdb=" CA TYR H 252 " pdb=" C TYR H 252 " pdb=" N PRO H 253 " pdb=" CA PRO H 253 " ideal model delta harmonic sigma weight residual 0.00 17.10 -17.10 0 5.00e+00 4.00e-02 1.17e+01 ... (remaining 5523 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 459 0.053 - 0.106: 451 0.106 - 0.158: 334 0.158 - 0.211: 136 0.211 - 0.264: 27 Chirality restraints: 1407 Sorted by residual: chirality pdb=" CB VAL R 126 " pdb=" CA VAL R 126 " pdb=" CG1 VAL R 126 " pdb=" CG2 VAL R 126 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA ILE B 120 " pdb=" N ILE B 120 " pdb=" C ILE B 120 " pdb=" CB ILE B 120 " both_signs ideal model delta sigma weight residual False 2.43 2.69 -0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA LEU B 79 " pdb=" N LEU B 79 " pdb=" C LEU B 79 " pdb=" CB LEU B 79 " both_signs ideal model delta sigma weight residual False 2.51 2.77 -0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 1404 not shown) Planarity restraints: 1587 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA CYS B 103 " 0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C CYS B 103 " -0.063 2.00e-02 2.50e+03 pdb=" O CYS B 103 " 0.023 2.00e-02 2.50e+03 pdb=" N ALA B 104 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 245 " -0.011 2.00e-02 2.50e+03 2.34e-02 5.48e+00 pdb=" C ASP A 245 " 0.040 2.00e-02 2.50e+03 pdb=" O ASP A 245 " -0.015 2.00e-02 2.50e+03 pdb=" N TYR A 246 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 196 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.95e+00 pdb=" C THR B 196 " -0.030 2.00e-02 2.50e+03 pdb=" O THR B 196 " 0.011 2.00e-02 2.50e+03 pdb=" N ARG B 197 " 0.010 2.00e-02 2.50e+03 ... (remaining 1584 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.65: 52 2.65 - 3.21: 8532 3.21 - 3.77: 14544 3.77 - 4.34: 21309 4.34 - 4.90: 33245 Nonbonded interactions: 77682 Sorted by model distance: nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.086 3.040 nonbonded pdb=" CD2 PHE R 70 " pdb=" OD2 ASP R 129 " model vdw 2.209 3.340 nonbonded pdb=" N ASP B 154 " pdb=" N ASN B 155 " model vdw 2.506 2.560 nonbonded pdb=" O THR H 161 " pdb=" OG1 THR H 260 " model vdw 2.520 3.040 nonbonded pdb=" N CYS B 166 " pdb=" O CYS B 166 " model vdw 2.561 2.496 ... (remaining 77677 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: 4.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.430 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 26.100 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 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 : 0.012 0.107 9283 Z= 0.935 Angle : 1.511 10.057 12602 Z= 1.178 Chirality : 0.103 0.264 1407 Planarity : 0.004 0.036 1587 Dihedral : 11.726 83.483 3373 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.12 % Allowed : 7.05 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.23), residues: 1120 helix: -0.91 (0.24), residues: 378 sheet: -0.86 (0.31), residues: 236 loop : -1.34 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 82 HIS 0.009 0.002 HIS B 311 PHE 0.021 0.002 PHE B 151 TYR 0.023 0.002 TYR H 207 ARG 0.006 0.001 ARG R 177 Details of bonding type rmsd hydrogen bonds : bond 0.16920 ( 461) hydrogen bonds : angle 7.87066 ( 1311) SS BOND : bond 0.00677 ( 3) SS BOND : angle 1.58961 ( 6) covalent geometry : bond 0.01231 ( 9279) covalent geometry : angle 1.51095 (12596) Misc. bond : bond 0.09443 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 256 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 63 GLU cc_start: 0.7576 (tt0) cc_final: 0.7325 (tm-30) REVERT: B 155 ASN cc_start: 0.7592 (t0) cc_final: 0.7196 (t0) REVERT: B 263 THR cc_start: 0.8886 (t) cc_final: 0.8659 (m) REVERT: A 6 SER cc_start: 0.8271 (p) cc_final: 0.7890 (p) REVERT: A 8 GLU cc_start: 0.8018 (mt-10) cc_final: 0.7688 (mm-30) REVERT: A 9 ASP cc_start: 0.7798 (m-30) cc_final: 0.7434 (m-30) REVERT: A 17 LYS cc_start: 0.7843 (mmtp) cc_final: 0.7326 (mtpt) REVERT: A 263 ARG cc_start: 0.7061 (ptm160) cc_final: 0.6829 (ptm160) REVERT: A 368 ARG cc_start: 0.7245 (OUTLIER) cc_final: 0.6937 (mtt-85) REVERT: A 372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6756 (tpt-90) REVERT: R 51 VAL cc_start: 0.7563 (t) cc_final: 0.7154 (p) REVERT: R 63 MET cc_start: 0.6860 (mmm) cc_final: 0.6296 (mtt) REVERT: R 109 ASN cc_start: 0.6708 (m-40) cc_final: 0.6060 (m-40) REVERT: R 161 LEU cc_start: 0.7349 (tp) cc_final: 0.7079 (tt) REVERT: R 163 PHE cc_start: 0.6569 (t80) cc_final: 0.6198 (t80) REVERT: R 182 ILE cc_start: 0.7803 (mt) cc_final: 0.7453 (mp) REVERT: P 8 PHE cc_start: 0.8219 (m-80) cc_final: 0.7845 (m-10) outliers start: 11 outliers final: 2 residues processed: 266 average time/residue: 1.1778 time to fit residues: 335.1235 Evaluate side-chains 176 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 173 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain A residue 368 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.7980 chunk 84 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 64 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN B 17 GLN B 266 HIS A 206 GLN A 211 ASN R 50 ASN R 68 ASN R 274 ASN R 301 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.183528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.125935 restraints weight = 10060.806| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 2.21 r_work: 0.3209 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3062 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8094 moved from start: 0.2473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9283 Z= 0.154 Angle : 0.595 7.228 12602 Z= 0.320 Chirality : 0.044 0.148 1407 Planarity : 0.004 0.049 1587 Dihedral : 4.490 48.606 1317 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.17 % Allowed : 15.32 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.24), residues: 1120 helix: 1.46 (0.25), residues: 390 sheet: -0.86 (0.29), residues: 246 loop : -0.59 (0.28), residues: 484 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.010 0.001 HIS A 213 PHE 0.024 0.002 PHE H 85 TYR 0.020 0.002 TYR R 272 ARG 0.006 0.001 ARG A 339 Details of bonding type rmsd hydrogen bonds : bond 0.05604 ( 461) hydrogen bonds : angle 5.43139 ( 1311) SS BOND : bond 0.00253 ( 3) SS BOND : angle 1.07352 ( 6) covalent geometry : bond 0.00329 ( 9279) covalent geometry : angle 0.59489 (12596) Misc. bond : bond 0.00041 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 205 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8594 (mp0) cc_final: 0.8372 (mt-10) REVERT: H 180 LYS cc_start: 0.8180 (ttpt) cc_final: 0.7960 (ttpp) REVERT: H 208 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.7093 (mtp180) REVERT: B 155 ASN cc_start: 0.8220 (t0) cc_final: 0.7499 (t0) REVERT: B 195 ASP cc_start: 0.7282 (p0) cc_final: 0.6985 (p0) REVERT: B 197 ARG cc_start: 0.7218 (mmt180) cc_final: 0.6966 (mmp-170) REVERT: B 219 ARG cc_start: 0.8285 (mmm-85) cc_final: 0.7964 (mmm-85) REVERT: B 226 GLU cc_start: 0.8600 (mt-10) cc_final: 0.8260 (mp0) REVERT: B 263 THR cc_start: 0.8924 (t) cc_final: 0.8715 (m) REVERT: G 18 GLN cc_start: 0.7209 (OUTLIER) cc_final: 0.6542 (tm-30) REVERT: A 17 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7309 (mtpt) REVERT: A 206 GLN cc_start: 0.7279 (tt0) cc_final: 0.6941 (tm-30) REVERT: A 263 ARG cc_start: 0.7170 (ptm160) cc_final: 0.6884 (ttp-110) REVERT: A 326 ASP cc_start: 0.7480 (t0) cc_final: 0.7250 (t70) REVERT: A 368 ARG cc_start: 0.7217 (OUTLIER) cc_final: 0.6801 (mtt180) REVERT: A 369 MET cc_start: 0.7250 (ttm) cc_final: 0.7036 (ttt) REVERT: A 372 ARG cc_start: 0.7233 (mtt90) cc_final: 0.6349 (tpp-160) REVERT: R 63 MET cc_start: 0.6537 (mmm) cc_final: 0.6022 (mtt) REVERT: R 90 PHE cc_start: 0.8663 (t80) cc_final: 0.8423 (t80) REVERT: R 109 ASN cc_start: 0.5833 (m-40) cc_final: 0.5579 (m-40) REVERT: R 121 TYR cc_start: 0.7377 (m-80) cc_final: 0.7166 (m-80) REVERT: R 161 LEU cc_start: 0.7058 (tp) cc_final: 0.6724 (tt) REVERT: R 163 PHE cc_start: 0.6529 (t80) cc_final: 0.6161 (t80) REVERT: R 305 TYR cc_start: 0.6574 (m-10) cc_final: 0.6371 (m-10) REVERT: P 8 PHE cc_start: 0.8151 (m-80) cc_final: 0.7704 (m-10) outliers start: 31 outliers final: 14 residues processed: 227 average time/residue: 1.1169 time to fit residues: 271.5924 Evaluate side-chains 190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain G residue 18 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 347 THR Chi-restraints excluded: chain A residue 348 CYS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 295 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 7 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.3980 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 13 optimal weight: 20.0000 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 0.0770 chunk 106 optimal weight: 0.8980 overall best weight: 0.8540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 99 GLN B 17 GLN A 277 GLN R 50 ASN R 96 ASN R 136 HIS R 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4064 r_free = 0.4064 target = 0.183084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.125643 restraints weight = 10125.094| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.11 r_work: 0.3180 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9283 Z= 0.154 Angle : 0.577 8.779 12602 Z= 0.307 Chirality : 0.044 0.255 1407 Planarity : 0.004 0.043 1587 Dihedral : 4.495 49.387 1316 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 3.98 % Allowed : 16.96 % Favored : 79.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.24), residues: 1120 helix: 1.79 (0.25), residues: 385 sheet: -0.71 (0.28), residues: 261 loop : -0.46 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.007 0.001 HIS A 213 PHE 0.033 0.002 PHE H 85 TYR 0.018 0.002 TYR B 105 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05090 ( 461) hydrogen bonds : angle 5.22409 ( 1311) SS BOND : bond 0.00298 ( 3) SS BOND : angle 1.08899 ( 6) covalent geometry : bond 0.00344 ( 9279) covalent geometry : angle 0.57696 (12596) Misc. bond : bond 0.00030 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 168 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8822 (OUTLIER) cc_final: 0.8567 (p) REVERT: H 106 GLU cc_start: 0.8585 (mp0) cc_final: 0.8370 (mt-10) REVERT: H 208 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.6917 (mtp180) REVERT: B 52 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.8141 (mtt90) REVERT: B 155 ASN cc_start: 0.8373 (t0) cc_final: 0.7852 (t0) REVERT: B 217 MET cc_start: 0.8279 (pmt) cc_final: 0.8067 (pmm) REVERT: B 219 ARG cc_start: 0.8292 (mmm-85) cc_final: 0.7832 (mmm-85) REVERT: B 226 GLU cc_start: 0.8595 (mt-10) cc_final: 0.8324 (mp0) REVERT: B 263 THR cc_start: 0.9004 (t) cc_final: 0.8753 (m) REVERT: G 20 LYS cc_start: 0.8156 (OUTLIER) cc_final: 0.7906 (mptm) REVERT: A 17 LYS cc_start: 0.8257 (mmtp) cc_final: 0.7349 (mtpt) REVERT: A 21 LYS cc_start: 0.7949 (mtpt) cc_final: 0.7494 (mtmm) REVERT: A 206 GLN cc_start: 0.7249 (tt0) cc_final: 0.6885 (tm-30) REVERT: A 254 ASN cc_start: 0.8158 (m-40) cc_final: 0.7918 (m110) REVERT: A 263 ARG cc_start: 0.7193 (ptm160) cc_final: 0.6927 (ttp-110) REVERT: A 290 LYS cc_start: 0.8237 (mppt) cc_final: 0.7968 (mptt) REVERT: A 326 ASP cc_start: 0.7565 (t0) cc_final: 0.7278 (t70) REVERT: A 372 ARG cc_start: 0.7177 (mtt90) cc_final: 0.6967 (mtm110) REVERT: R 63 MET cc_start: 0.6523 (mmm) cc_final: 0.6087 (mtt) REVERT: R 81 MET cc_start: 0.7412 (ttm) cc_final: 0.7164 (ptp) REVERT: R 161 LEU cc_start: 0.7060 (tp) cc_final: 0.6707 (tt) REVERT: R 163 PHE cc_start: 0.6514 (t80) cc_final: 0.6160 (t80) REVERT: R 205 TYR cc_start: 0.7786 (t80) cc_final: 0.6833 (t80) REVERT: P 8 PHE cc_start: 0.8234 (m-80) cc_final: 0.7788 (m-10) outliers start: 39 outliers final: 19 residues processed: 192 average time/residue: 1.7626 time to fit residues: 361.7344 Evaluate side-chains 173 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 150 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 179 SER Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain B residue 52 ARG Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 196 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 262 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 214 MET Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain R residue 72 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 83 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 57 optimal weight: 0.0970 chunk 61 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 38 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN A 22 GLN A 277 GLN R 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4082 r_free = 0.4082 target = 0.184935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.128108 restraints weight = 10026.851| |-----------------------------------------------------------------------------| r_work (start): 0.3330 rms_B_bonded: 2.30 r_work: 0.3159 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3011 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9283 Z= 0.128 Angle : 0.532 7.749 12602 Z= 0.284 Chirality : 0.042 0.141 1407 Planarity : 0.004 0.041 1587 Dihedral : 4.077 26.636 1312 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 4.29 % Allowed : 17.36 % Favored : 78.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.24), residues: 1120 helix: 1.91 (0.25), residues: 388 sheet: -0.74 (0.28), residues: 274 loop : -0.22 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.008 0.001 HIS A 213 PHE 0.030 0.002 PHE R 90 TYR 0.016 0.001 TYR B 59 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 461) hydrogen bonds : angle 5.01419 ( 1311) SS BOND : bond 0.00306 ( 3) SS BOND : angle 0.93988 ( 6) covalent geometry : bond 0.00277 ( 9279) covalent geometry : angle 0.53200 (12596) Misc. bond : bond 0.00028 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 173 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8850 (OUTLIER) cc_final: 0.8604 (p) REVERT: H 106 GLU cc_start: 0.8632 (mp0) cc_final: 0.8395 (mt-10) REVERT: B 155 ASN cc_start: 0.8420 (t0) cc_final: 0.8121 (t0) REVERT: B 217 MET cc_start: 0.8281 (pmt) cc_final: 0.8027 (pmm) REVERT: B 219 ARG cc_start: 0.8311 (mmm-85) cc_final: 0.7799 (mmm-85) REVERT: B 226 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8301 (mp0) REVERT: B 247 ASP cc_start: 0.7756 (t0) cc_final: 0.7320 (t0) REVERT: B 263 THR cc_start: 0.8981 (t) cc_final: 0.8722 (m) REVERT: G 20 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7891 (mptm) REVERT: A 17 LYS cc_start: 0.8216 (mmtp) cc_final: 0.7332 (mtpt) REVERT: A 21 LYS cc_start: 0.7879 (mtpt) cc_final: 0.7434 (mtmm) REVERT: A 206 GLN cc_start: 0.7256 (tt0) cc_final: 0.6864 (tm-30) REVERT: A 254 ASN cc_start: 0.8146 (m-40) cc_final: 0.7879 (m110) REVERT: A 263 ARG cc_start: 0.7150 (ptm160) cc_final: 0.6861 (ttp-110) REVERT: A 290 LYS cc_start: 0.8301 (mppt) cc_final: 0.8045 (mptp) REVERT: A 326 ASP cc_start: 0.7625 (t0) cc_final: 0.7331 (t70) REVERT: A 368 ARG cc_start: 0.7336 (OUTLIER) cc_final: 0.6827 (mtt180) REVERT: R 63 MET cc_start: 0.6437 (mmm) cc_final: 0.6083 (mtt) REVERT: R 85 ASN cc_start: 0.6334 (t0) cc_final: 0.5793 (t160) REVERT: R 89 ASN cc_start: 0.7275 (m-40) cc_final: 0.6618 (m-40) REVERT: R 161 LEU cc_start: 0.7078 (tp) cc_final: 0.6764 (tt) REVERT: R 163 PHE cc_start: 0.6472 (t80) cc_final: 0.6119 (t80) REVERT: R 205 TYR cc_start: 0.7809 (t80) cc_final: 0.6786 (t80) REVERT: R 262 LEU cc_start: 0.7618 (tp) cc_final: 0.7187 (tp) REVERT: P 8 PHE cc_start: 0.8275 (m-80) cc_final: 0.7831 (m-10) outliers start: 42 outliers final: 15 residues processed: 204 average time/residue: 1.1971 time to fit residues: 260.8590 Evaluate side-chains 179 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 161 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 40 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 103 optimal weight: 6.9990 chunk 77 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 1 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 30 GLN H 196 GLN B 17 GLN B 259 GLN A 213 HIS A 229 GLN A 277 GLN R 50 ASN R 68 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.180008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.121955 restraints weight = 10071.262| |-----------------------------------------------------------------------------| r_work (start): 0.3260 rms_B_bonded: 2.15 r_work: 0.3096 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2949 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8210 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 9283 Z= 0.232 Angle : 0.624 9.812 12602 Z= 0.328 Chirality : 0.045 0.165 1407 Planarity : 0.004 0.038 1587 Dihedral : 4.383 28.322 1311 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 5.01 % Allowed : 17.98 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.24), residues: 1120 helix: 1.67 (0.25), residues: 384 sheet: -0.68 (0.28), residues: 281 loop : -0.27 (0.29), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 169 HIS 0.004 0.001 HIS A 345 PHE 0.035 0.002 PHE H 85 TYR 0.018 0.002 TYR B 105 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.05175 ( 461) hydrogen bonds : angle 5.27730 ( 1311) SS BOND : bond 0.00332 ( 3) SS BOND : angle 1.32031 ( 6) covalent geometry : bond 0.00541 ( 9279) covalent geometry : angle 0.62393 (12596) Misc. bond : bond 0.00069 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 171 time to evaluate : 1.047 Fit side-chains revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8605 (mp0) cc_final: 0.8374 (mt-10) REVERT: B 155 ASN cc_start: 0.8542 (t0) cc_final: 0.8127 (t0) REVERT: B 176 GLN cc_start: 0.8581 (mt0) cc_final: 0.8368 (tt0) REVERT: B 217 MET cc_start: 0.8359 (pmt) cc_final: 0.8085 (pmm) REVERT: B 219 ARG cc_start: 0.8433 (mmm-85) cc_final: 0.7863 (mmm-85) REVERT: B 226 GLU cc_start: 0.8675 (mt-10) cc_final: 0.8290 (mp0) REVERT: B 258 ASP cc_start: 0.8171 (t0) cc_final: 0.7740 (t70) REVERT: B 273 ILE cc_start: 0.9069 (OUTLIER) cc_final: 0.8806 (mp) REVERT: G 20 LYS cc_start: 0.8174 (OUTLIER) cc_final: 0.7907 (mptm) REVERT: A 17 LYS cc_start: 0.8280 (mmtp) cc_final: 0.7442 (mtpt) REVERT: A 21 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7513 (mtmm) REVERT: A 26 ASP cc_start: 0.8183 (m-30) cc_final: 0.7626 (m-30) REVERT: A 206 GLN cc_start: 0.7253 (tt0) cc_final: 0.6921 (tm-30) REVERT: A 229 GLN cc_start: 0.8603 (OUTLIER) cc_final: 0.8332 (pp30) REVERT: A 290 LYS cc_start: 0.8481 (mppt) cc_final: 0.8224 (mptp) REVERT: A 326 ASP cc_start: 0.7666 (t0) cc_final: 0.7371 (t70) REVERT: A 368 ARG cc_start: 0.7375 (OUTLIER) cc_final: 0.6827 (mtt180) REVERT: R 63 MET cc_start: 0.6548 (mmm) cc_final: 0.6199 (mtt) REVERT: R 68 ASN cc_start: 0.7841 (m-40) cc_final: 0.7638 (m110) REVERT: R 89 ASN cc_start: 0.7347 (m-40) cc_final: 0.6702 (m-40) REVERT: R 161 LEU cc_start: 0.7078 (tp) cc_final: 0.6763 (tp) REVERT: R 163 PHE cc_start: 0.6561 (t80) cc_final: 0.6227 (t80) REVERT: R 205 TYR cc_start: 0.7818 (t80) cc_final: 0.6777 (t80) REVERT: R 262 LEU cc_start: 0.7736 (tp) cc_final: 0.7296 (tp) REVERT: P 8 PHE cc_start: 0.8304 (m-80) cc_final: 0.7992 (m-80) outliers start: 49 outliers final: 21 residues processed: 203 average time/residue: 1.1149 time to fit residues: 242.4612 Evaluate side-chains 188 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 163 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 197 ARG Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 273 ILE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 207 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 17 optimal weight: 0.7980 chunk 91 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 88 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 76 optimal weight: 5.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 229 GLN A 277 GLN R 50 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.180713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.122813 restraints weight = 10032.481| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.17 r_work: 0.3120 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 9283 Z= 0.176 Angle : 0.571 9.286 12602 Z= 0.303 Chirality : 0.044 0.156 1407 Planarity : 0.004 0.037 1587 Dihedral : 4.300 26.558 1311 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.09 % Allowed : 19.41 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.24), residues: 1120 helix: 1.73 (0.25), residues: 387 sheet: -0.70 (0.28), residues: 285 loop : -0.25 (0.29), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.007 0.001 HIS A 213 PHE 0.041 0.002 PHE H 85 TYR 0.015 0.002 TYR B 59 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04837 ( 461) hydrogen bonds : angle 5.19778 ( 1311) SS BOND : bond 0.00337 ( 3) SS BOND : angle 1.25020 ( 6) covalent geometry : bond 0.00401 ( 9279) covalent geometry : angle 0.57010 (12596) Misc. bond : bond 0.00042 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 169 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 80 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8717 (p) REVERT: H 106 GLU cc_start: 0.8598 (mp0) cc_final: 0.8376 (mt-10) REVERT: B 155 ASN cc_start: 0.8538 (t0) cc_final: 0.8117 (t0) REVERT: B 176 GLN cc_start: 0.8536 (mt0) cc_final: 0.8321 (tt0) REVERT: B 217 MET cc_start: 0.8392 (pmt) cc_final: 0.8132 (pmm) REVERT: B 219 ARG cc_start: 0.8392 (mmm-85) cc_final: 0.7858 (mmm-85) REVERT: B 226 GLU cc_start: 0.8691 (mt-10) cc_final: 0.8280 (mp0) REVERT: B 258 ASP cc_start: 0.8115 (t0) cc_final: 0.7660 (t70) REVERT: G 20 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7901 (mptm) REVERT: A 17 LYS cc_start: 0.8254 (mmtp) cc_final: 0.7431 (mtpt) REVERT: A 21 LYS cc_start: 0.7915 (mtpt) cc_final: 0.7477 (mtmm) REVERT: A 26 ASP cc_start: 0.8133 (m-30) cc_final: 0.7557 (m-30) REVERT: A 206 GLN cc_start: 0.7214 (tt0) cc_final: 0.6909 (tm-30) REVERT: A 213 HIS cc_start: 0.7899 (t70) cc_final: 0.7662 (m-70) REVERT: A 229 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8232 (pp30) REVERT: A 290 LYS cc_start: 0.8515 (mppt) cc_final: 0.8255 (mptp) REVERT: A 326 ASP cc_start: 0.7725 (t0) cc_final: 0.7436 (t70) REVERT: A 368 ARG cc_start: 0.7363 (OUTLIER) cc_final: 0.6893 (mtt-85) REVERT: R 63 MET cc_start: 0.6540 (mmm) cc_final: 0.6224 (mtt) REVERT: R 89 ASN cc_start: 0.7318 (m-40) cc_final: 0.6738 (m-40) REVERT: R 161 LEU cc_start: 0.7099 (tp) cc_final: 0.6835 (tp) REVERT: R 163 PHE cc_start: 0.6528 (t80) cc_final: 0.6199 (t80) REVERT: R 205 TYR cc_start: 0.7834 (t80) cc_final: 0.6812 (t80) REVERT: R 299 MET cc_start: 0.7421 (ptm) cc_final: 0.6840 (ptt) REVERT: R 300 TYR cc_start: 0.6347 (m-10) cc_final: 0.5840 (m-10) REVERT: R 314 LEU cc_start: 0.6171 (OUTLIER) cc_final: 0.5894 (mt) REVERT: P 8 PHE cc_start: 0.8327 (m-80) cc_final: 0.7991 (m-80) outliers start: 40 outliers final: 21 residues processed: 198 average time/residue: 1.2772 time to fit residues: 271.0484 Evaluate side-chains 188 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 162 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 227 SER Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 207 LEU Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 63 optimal weight: 3.9990 chunk 110 optimal weight: 7.9990 chunk 41 optimal weight: 0.5980 chunk 61 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN A 229 GLN A 250 GLN A 254 ASN A 275 ASN A 277 GLN R 68 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.180554 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.122579 restraints weight = 10165.425| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.13 r_work: 0.3109 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.3888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 9283 Z= 0.208 Angle : 0.596 9.748 12602 Z= 0.316 Chirality : 0.045 0.219 1407 Planarity : 0.004 0.037 1587 Dihedral : 4.392 26.782 1311 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 4.49 % Allowed : 18.49 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.24), residues: 1120 helix: 1.66 (0.25), residues: 383 sheet: -0.65 (0.29), residues: 275 loop : -0.26 (0.29), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 169 HIS 0.008 0.001 HIS A 213 PHE 0.040 0.002 PHE H 85 TYR 0.017 0.002 TYR R 305 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04992 ( 461) hydrogen bonds : angle 5.23318 ( 1311) SS BOND : bond 0.00356 ( 3) SS BOND : angle 1.88691 ( 6) covalent geometry : bond 0.00483 ( 9279) covalent geometry : angle 0.59508 (12596) Misc. bond : bond 0.00048 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 159 time to evaluate : 0.930 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 106 GLU cc_start: 0.8643 (mp0) cc_final: 0.8409 (mt-10) REVERT: H 208 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.6848 (mtp180) REVERT: B 155 ASN cc_start: 0.8582 (t0) cc_final: 0.8177 (t0) REVERT: B 176 GLN cc_start: 0.8524 (mt0) cc_final: 0.8323 (tt0) REVERT: B 217 MET cc_start: 0.8412 (pmt) cc_final: 0.8194 (pmm) REVERT: B 219 ARG cc_start: 0.8408 (mmm-85) cc_final: 0.7870 (mmm-85) REVERT: B 226 GLU cc_start: 0.8622 (mt-10) cc_final: 0.8207 (mp0) REVERT: B 258 ASP cc_start: 0.8129 (t0) cc_final: 0.7733 (t70) REVERT: G 18 GLN cc_start: 0.7363 (mm-40) cc_final: 0.6893 (tm-30) REVERT: G 20 LYS cc_start: 0.8186 (OUTLIER) cc_final: 0.7913 (mptm) REVERT: A 17 LYS cc_start: 0.8299 (mmtp) cc_final: 0.7496 (mtpt) REVERT: A 21 LYS cc_start: 0.7958 (mtpt) cc_final: 0.7522 (mtmm) REVERT: A 26 ASP cc_start: 0.8122 (m-30) cc_final: 0.7525 (m-30) REVERT: A 206 GLN cc_start: 0.7213 (tt0) cc_final: 0.6896 (tm-30) REVERT: A 229 GLN cc_start: 0.8592 (OUTLIER) cc_final: 0.8283 (pp30) REVERT: A 290 LYS cc_start: 0.8555 (mppt) cc_final: 0.8324 (mptp) REVERT: A 326 ASP cc_start: 0.7718 (t0) cc_final: 0.7441 (t70) REVERT: A 368 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.6816 (mtt180) REVERT: R 63 MET cc_start: 0.6562 (mmm) cc_final: 0.6244 (mtt) REVERT: R 89 ASN cc_start: 0.7380 (m-40) cc_final: 0.6768 (m-40) REVERT: R 161 LEU cc_start: 0.7125 (tp) cc_final: 0.6875 (tp) REVERT: R 163 PHE cc_start: 0.6543 (t80) cc_final: 0.6232 (t80) REVERT: R 205 TYR cc_start: 0.7822 (t80) cc_final: 0.6775 (t80) REVERT: R 299 MET cc_start: 0.7404 (ptm) cc_final: 0.7152 (ptm) REVERT: R 300 TYR cc_start: 0.6332 (m-10) cc_final: 0.6027 (m-10) REVERT: R 314 LEU cc_start: 0.6122 (OUTLIER) cc_final: 0.5808 (mt) REVERT: P 8 PHE cc_start: 0.8296 (m-80) cc_final: 0.7973 (m-80) outliers start: 44 outliers final: 25 residues processed: 193 average time/residue: 1.4947 time to fit residues: 309.5497 Evaluate side-chains 191 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 161 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 23 GLU Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 208 ARG Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 20 LYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain A residue 4 THR Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 47 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 282 GLU Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 104 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 chunk 97 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 52 optimal weight: 0.0870 chunk 27 optimal weight: 0.8980 overall best weight: 0.7158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN A 213 HIS A 275 ASN A 277 GLN R 68 ASN R 96 ASN R 274 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.182811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.125067 restraints weight = 10197.502| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.15 r_work: 0.3216 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9283 Z= 0.141 Angle : 0.559 9.334 12602 Z= 0.294 Chirality : 0.043 0.197 1407 Planarity : 0.004 0.038 1587 Dihedral : 4.224 25.076 1311 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 3.17 % Allowed : 19.82 % Favored : 77.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1120 helix: 1.82 (0.25), residues: 382 sheet: -0.59 (0.29), residues: 273 loop : -0.14 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.008 0.001 HIS A 213 PHE 0.028 0.001 PHE H 85 TYR 0.015 0.001 TYR R 305 ARG 0.008 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04609 ( 461) hydrogen bonds : angle 5.07774 ( 1311) SS BOND : bond 0.00291 ( 3) SS BOND : angle 1.51737 ( 6) covalent geometry : bond 0.00312 ( 9279) covalent geometry : angle 0.55780 (12596) Misc. bond : bond 0.00020 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.928 Fit side-chains revert: symmetry clash REVERT: H 63 GLU cc_start: 0.8449 (tt0) cc_final: 0.7876 (pt0) REVERT: H 80 THR cc_start: 0.8960 (OUTLIER) cc_final: 0.8692 (p) REVERT: H 106 GLU cc_start: 0.8607 (mp0) cc_final: 0.8381 (mt-10) REVERT: B 155 ASN cc_start: 0.8549 (t0) cc_final: 0.8034 (t0) REVERT: B 214 ARG cc_start: 0.8228 (ptp90) cc_final: 0.7825 (mpp80) REVERT: B 219 ARG cc_start: 0.8369 (mmm-85) cc_final: 0.7915 (mmm-85) REVERT: B 226 GLU cc_start: 0.8636 (mt-10) cc_final: 0.8229 (mp0) REVERT: B 258 ASP cc_start: 0.8076 (t0) cc_final: 0.7655 (t70) REVERT: B 263 THR cc_start: 0.9064 (t) cc_final: 0.8724 (m) REVERT: B 266 HIS cc_start: 0.7559 (t70) cc_final: 0.6629 (OUTLIER) REVERT: A 17 LYS cc_start: 0.8344 (mmtp) cc_final: 0.7565 (mtpt) REVERT: A 21 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7487 (mtmm) REVERT: A 26 ASP cc_start: 0.8099 (m-30) cc_final: 0.7537 (m-30) REVERT: A 206 GLN cc_start: 0.7202 (tt0) cc_final: 0.6911 (tm-30) REVERT: A 213 HIS cc_start: 0.7780 (OUTLIER) cc_final: 0.7379 (t-170) REVERT: A 229 GLN cc_start: 0.8557 (tm-30) cc_final: 0.8255 (pp30) REVERT: A 290 LYS cc_start: 0.8549 (mppt) cc_final: 0.8321 (mptp) REVERT: A 326 ASP cc_start: 0.7727 (t0) cc_final: 0.7460 (t70) REVERT: A 368 ARG cc_start: 0.7409 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: R 63 MET cc_start: 0.6545 (mmm) cc_final: 0.6284 (mtt) REVERT: R 68 ASN cc_start: 0.7970 (m-40) cc_final: 0.7766 (m110) REVERT: R 85 ASN cc_start: 0.6482 (t0) cc_final: 0.5924 (t160) REVERT: R 89 ASN cc_start: 0.7358 (m-40) cc_final: 0.6721 (m-40) REVERT: R 161 LEU cc_start: 0.7163 (tp) cc_final: 0.6924 (tp) REVERT: R 163 PHE cc_start: 0.6551 (t80) cc_final: 0.6216 (t80) REVERT: R 205 TYR cc_start: 0.7860 (t80) cc_final: 0.6838 (t80) REVERT: R 299 MET cc_start: 0.7488 (ptm) cc_final: 0.7279 (ptm) REVERT: R 314 LEU cc_start: 0.6255 (OUTLIER) cc_final: 0.5895 (mt) REVERT: P 8 PHE cc_start: 0.8330 (m-80) cc_final: 0.8053 (m-80) outliers start: 31 outliers final: 20 residues processed: 191 average time/residue: 1.3540 time to fit residues: 275.7224 Evaluate side-chains 186 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain G residue 25 ILE Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 100 TYR Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 70 optimal weight: 0.8980 chunk 74 optimal weight: 4.9990 chunk 98 optimal weight: 8.9990 chunk 101 optimal weight: 0.0770 chunk 44 optimal weight: 3.9990 chunk 109 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 57 optimal weight: 0.3980 chunk 6 optimal weight: 1.9990 chunk 110 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 GLN H 196 GLN B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 277 GLN R 96 ASN R 274 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.180936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.123273 restraints weight = 9991.592| |-----------------------------------------------------------------------------| r_work (start): 0.3284 rms_B_bonded: 2.10 r_work: 0.3141 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3001 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3001 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.4058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9283 Z= 0.194 Angle : 0.597 9.468 12602 Z= 0.314 Chirality : 0.045 0.187 1407 Planarity : 0.004 0.045 1587 Dihedral : 4.353 26.047 1311 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.37 % Allowed : 19.82 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.25), residues: 1120 helix: 1.66 (0.25), residues: 384 sheet: -0.51 (0.29), residues: 276 loop : -0.17 (0.29), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 169 HIS 0.005 0.001 HIS A 213 PHE 0.031 0.002 PHE H 85 TYR 0.021 0.002 TYR R 300 ARG 0.011 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04909 ( 461) hydrogen bonds : angle 5.17777 ( 1311) SS BOND : bond 0.00327 ( 3) SS BOND : angle 1.41653 ( 6) covalent geometry : bond 0.00447 ( 9279) covalent geometry : angle 0.59614 (12596) Misc. bond : bond 0.00049 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 164 time to evaluate : 1.235 Fit side-chains revert: symmetry clash REVERT: H 60 LYS cc_start: 0.8971 (mmtm) cc_final: 0.8717 (mppt) REVERT: H 63 GLU cc_start: 0.8505 (tt0) cc_final: 0.7845 (pt0) REVERT: H 106 GLU cc_start: 0.8611 (mp0) cc_final: 0.8386 (mt-10) REVERT: B 155 ASN cc_start: 0.8582 (t0) cc_final: 0.8328 (t0) REVERT: B 219 ARG cc_start: 0.8353 (mmm-85) cc_final: 0.7864 (mmm-85) REVERT: B 226 GLU cc_start: 0.8593 (mt-10) cc_final: 0.8147 (mp0) REVERT: B 258 ASP cc_start: 0.8114 (t0) cc_final: 0.7750 (t70) REVERT: B 263 THR cc_start: 0.9115 (t) cc_final: 0.8721 (m) REVERT: B 266 HIS cc_start: 0.7564 (t70) cc_final: 0.6762 (OUTLIER) REVERT: A 17 LYS cc_start: 0.8315 (mmtp) cc_final: 0.7516 (mtpt) REVERT: A 26 ASP cc_start: 0.8076 (m-30) cc_final: 0.7480 (m-30) REVERT: A 206 GLN cc_start: 0.7159 (tt0) cc_final: 0.6848 (tm-30) REVERT: A 213 HIS cc_start: 0.7869 (m-70) cc_final: 0.7593 (t-170) REVERT: A 229 GLN cc_start: 0.8649 (tm-30) cc_final: 0.8399 (pp30) REVERT: A 274 LEU cc_start: 0.7857 (mp) cc_final: 0.7644 (mm) REVERT: A 290 LYS cc_start: 0.8614 (mppt) cc_final: 0.8085 (ttpp) REVERT: A 326 ASP cc_start: 0.7685 (t0) cc_final: 0.7420 (t70) REVERT: A 368 ARG cc_start: 0.7374 (OUTLIER) cc_final: 0.6885 (mtt-85) REVERT: R 63 MET cc_start: 0.6574 (mmm) cc_final: 0.6327 (mtt) REVERT: R 85 ASN cc_start: 0.6565 (t0) cc_final: 0.5942 (t160) REVERT: R 89 ASN cc_start: 0.7334 (m-40) cc_final: 0.6695 (m-40) REVERT: R 161 LEU cc_start: 0.7124 (tp) cc_final: 0.6902 (tp) REVERT: R 163 PHE cc_start: 0.6580 (t80) cc_final: 0.6308 (t80) REVERT: R 205 TYR cc_start: 0.7850 (t80) cc_final: 0.6801 (t80) REVERT: R 314 LEU cc_start: 0.6250 (OUTLIER) cc_final: 0.5881 (mt) REVERT: P 8 PHE cc_start: 0.8317 (m-80) cc_final: 0.8045 (m-80) outliers start: 33 outliers final: 23 residues processed: 190 average time/residue: 1.2343 time to fit residues: 250.9940 Evaluate side-chains 188 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 164 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 73 ASN Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 chunk 87 optimal weight: 8.9990 chunk 23 optimal weight: 0.9990 chunk 108 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 0.9980 chunk 32 optimal weight: 0.4980 chunk 91 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 GLN H 196 GLN B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 59 ASN A 213 HIS A 275 ASN A 277 GLN R 68 ASN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.182444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.124927 restraints weight = 10015.358| |-----------------------------------------------------------------------------| r_work (start): 0.3301 rms_B_bonded: 2.11 r_work: 0.3158 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.4162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 9283 Z= 0.155 Angle : 0.580 9.636 12602 Z= 0.304 Chirality : 0.044 0.190 1407 Planarity : 0.004 0.040 1587 Dihedral : 4.274 25.008 1311 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.55 % Allowed : 20.74 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.25), residues: 1120 helix: 1.65 (0.25), residues: 385 sheet: -0.39 (0.29), residues: 279 loop : -0.15 (0.29), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.006 0.001 HIS A 213 PHE 0.031 0.001 PHE H 85 TYR 0.026 0.002 TYR R 300 ARG 0.012 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04691 ( 461) hydrogen bonds : angle 5.07584 ( 1311) SS BOND : bond 0.00299 ( 3) SS BOND : angle 1.30725 ( 6) covalent geometry : bond 0.00351 ( 9279) covalent geometry : angle 0.57953 (12596) Misc. bond : bond 0.00033 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2240 Ramachandran restraints generated. 1120 Oldfield, 0 Emsley, 1120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 165 time to evaluate : 1.048 Fit side-chains revert: symmetry clash REVERT: H 63 GLU cc_start: 0.8497 (tt0) cc_final: 0.7855 (pt0) REVERT: H 80 THR cc_start: 0.8958 (OUTLIER) cc_final: 0.8693 (p) REVERT: H 106 GLU cc_start: 0.8603 (mp0) cc_final: 0.8362 (mt-10) REVERT: B 155 ASN cc_start: 0.8552 (t0) cc_final: 0.8312 (t0) REVERT: B 219 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.7823 (mmm-85) REVERT: B 226 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8213 (mp0) REVERT: B 258 ASP cc_start: 0.8025 (t0) cc_final: 0.7596 (t70) REVERT: B 263 THR cc_start: 0.9041 (t) cc_final: 0.8718 (m) REVERT: B 266 HIS cc_start: 0.7437 (t70) cc_final: 0.6808 (OUTLIER) REVERT: A 17 LYS cc_start: 0.8249 (mmtp) cc_final: 0.7443 (mtpt) REVERT: A 21 LYS cc_start: 0.7859 (mtpt) cc_final: 0.7410 (mtmm) REVERT: A 26 ASP cc_start: 0.8077 (m-30) cc_final: 0.7483 (m-30) REVERT: A 206 GLN cc_start: 0.7162 (tt0) cc_final: 0.6830 (tm-30) REVERT: A 213 HIS cc_start: 0.7827 (OUTLIER) cc_final: 0.7473 (t-170) REVERT: A 229 GLN cc_start: 0.8680 (tm-30) cc_final: 0.8444 (pp30) REVERT: A 290 LYS cc_start: 0.8614 (mppt) cc_final: 0.8078 (ttpp) REVERT: A 326 ASP cc_start: 0.7673 (t0) cc_final: 0.7399 (t70) REVERT: A 368 ARG cc_start: 0.7339 (OUTLIER) cc_final: 0.6805 (mtt180) REVERT: R 63 MET cc_start: 0.6496 (mmm) cc_final: 0.6261 (mtt) REVERT: R 68 ASN cc_start: 0.7888 (m-40) cc_final: 0.7683 (m110) REVERT: R 85 ASN cc_start: 0.6452 (t0) cc_final: 0.5978 (t160) REVERT: R 89 ASN cc_start: 0.7163 (m-40) cc_final: 0.6670 (m-40) REVERT: R 163 PHE cc_start: 0.6543 (t80) cc_final: 0.6253 (t80) REVERT: R 205 TYR cc_start: 0.7835 (t80) cc_final: 0.6780 (t80) REVERT: R 300 TYR cc_start: 0.6117 (m-10) cc_final: 0.5851 (m-10) REVERT: R 314 LEU cc_start: 0.6227 (OUTLIER) cc_final: 0.5861 (mt) REVERT: P 8 PHE cc_start: 0.8289 (m-80) cc_final: 0.7970 (m-80) outliers start: 25 outliers final: 19 residues processed: 184 average time/residue: 1.1250 time to fit residues: 221.5632 Evaluate side-chains 180 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 158 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 29 VAL Chi-restraints excluded: chain H residue 72 SER Chi-restraints excluded: chain H residue 80 THR Chi-restraints excluded: chain H residue 172 VAL Chi-restraints excluded: chain H residue 203 GLN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain B residue 98 SER Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 153 ASP Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 210 LEU Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 317 CYS Chi-restraints excluded: chain A residue 6 SER Chi-restraints excluded: chain A residue 213 HIS Chi-restraints excluded: chain A residue 368 ARG Chi-restraints excluded: chain R residue 72 VAL Chi-restraints excluded: chain R residue 266 ILE Chi-restraints excluded: chain R residue 314 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 60 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 100 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 GLN B 17 GLN ** B 259 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 275 ASN A 277 GLN ** R 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 274 ASN ** R 309 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.182742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125408 restraints weight = 10000.993| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 2.13 r_work: 0.3182 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.4197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9283 Z= 0.141 Angle : 0.579 9.390 12602 Z= 0.305 Chirality : 0.043 0.188 1407 Planarity : 0.004 0.055 1587 Dihedral : 4.237 24.894 1311 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.15 % Allowed : 21.35 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.25), residues: 1120 helix: 1.69 (0.25), residues: 384 sheet: -0.42 (0.29), residues: 286 loop : -0.04 (0.30), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.009 0.001 HIS A 213 PHE 0.024 0.001 PHE H 85 TYR 0.023 0.002 TYR R 300 ARG 0.013 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.04592 ( 461) hydrogen bonds : angle 5.05678 ( 1311) SS BOND : bond 0.00284 ( 3) SS BOND : angle 1.18302 ( 6) covalent geometry : bond 0.00311 ( 9279) covalent geometry : angle 0.57851 (12596) Misc. bond : bond 0.00025 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9120.10 seconds wall clock time: 161 minutes 1.16 seconds (9661.16 seconds total)