Starting phenix.real_space_refine on Sat Jun 7 07:53:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh0_39278/06_2025/8yh0_39278.cif" } resolution = 2.86 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= -0.004 sd= 1.047 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 66 5.16 5 C 5561 2.51 5 N 1463 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.25, per 1000 atoms: 0.60 Number of scatterers: 8693 At special positions: 0 Unit cell: (90.37, 123.936, 123.936, 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 66 16.00 O 1603 8.00 N 1463 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " 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=0, symmetry=0 Time building additional restraints: 2.33 Conformation dependent library (CDL) restraints added in 949.6 milliseconds 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2066 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 37.8% alpha, 22.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'R' and resid 9 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.534A pdb=" N CYS R 83 " --> pdb=" O HIS R 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.533A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.688A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.880A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.572A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.817A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.705A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.847A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.955A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.910A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.138A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.815A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.555A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.189A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1212 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: 2.37 Time building geometry restraints manager: 2.67 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1389 1.31 - 1.44: 2459 1.44 - 1.56: 4930 1.56 - 1.69: 0 1.69 - 1.82: 98 Bond restraints: 8876 Sorted by residual: bond pdb=" C5 NEC R 801 " pdb=" N7 NEC R 801 " ideal model delta sigma weight residual 1.370 1.524 -0.154 2.00e-02 2.50e+03 5.89e+01 bond pdb=" C6 NEC R 801 " pdb=" N6 NEC R 801 " ideal model delta sigma weight residual 1.334 1.451 -0.117 2.00e-02 2.50e+03 3.41e+01 bond pdb=" C5' NEC R 801 " pdb=" N5' NEC R 801 " ideal model delta sigma weight residual 1.335 1.451 -0.116 2.00e-02 2.50e+03 3.38e+01 bond pdb=" C8 NEC R 801 " pdb=" N9 NEC R 801 " ideal model delta sigma weight residual 1.370 1.254 0.116 2.00e-02 2.50e+03 3.34e+01 bond pdb=" C4 NEC R 801 " pdb=" C5 NEC R 801 " ideal model delta sigma weight residual 1.385 1.479 -0.094 2.00e-02 2.50e+03 2.22e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 11957 3.00 - 6.00: 49 6.00 - 9.00: 7 9.00 - 11.99: 7 11.99 - 14.99: 1 Bond angle restraints: 12021 Sorted by residual: angle pdb=" N PRO G 53 " pdb=" CA PRO G 53 " pdb=" C PRO G 53 " ideal model delta sigma weight residual 111.14 121.41 -10.27 1.56e+00 4.11e-01 4.34e+01 angle pdb=" C4 NEC R 801 " pdb=" N9 NEC R 801 " pdb=" C8 NEC R 801 " ideal model delta sigma weight residual 106.36 121.35 -14.99 3.00e+00 1.11e-01 2.50e+01 angle pdb=" N LYS A 349 " pdb=" CA LYS A 349 " pdb=" C LYS A 349 " ideal model delta sigma weight residual 113.19 108.87 4.32 1.19e+00 7.06e-01 1.32e+01 angle pdb=" N ILE R 185 " pdb=" CA ILE R 185 " pdb=" C ILE R 185 " ideal model delta sigma weight residual 111.62 108.77 2.85 7.90e-01 1.60e+00 1.30e+01 angle pdb=" N VAL R 121 " pdb=" CA VAL R 121 " pdb=" C VAL R 121 " ideal model delta sigma weight residual 112.96 109.38 3.58 1.00e+00 1.00e+00 1.28e+01 ... (remaining 12016 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 4673 15.55 - 31.10: 478 31.10 - 46.65: 104 46.65 - 62.20: 14 62.20 - 77.75: 5 Dihedral angle restraints: 5274 sinusoidal: 2072 harmonic: 3202 Sorted by residual: dihedral pdb=" CA TYR S 178 " pdb=" C TYR S 178 " pdb=" N ARG S 179 " pdb=" CA ARG S 179 " ideal model delta harmonic sigma weight residual 180.00 155.88 24.12 0 5.00e+00 4.00e-02 2.33e+01 dihedral pdb=" CB CYS S 147 " pdb=" SG CYS S 147 " pdb=" SG CYS S 217 " pdb=" CB CYS S 217 " ideal model delta sinusoidal sigma weight residual 93.00 132.98 -39.98 1 1.00e+01 1.00e-02 2.24e+01 dihedral pdb=" CA PHE A 267 " pdb=" C PHE A 267 " pdb=" N LEU A 268 " pdb=" CA LEU A 268 " ideal model delta harmonic sigma weight residual 180.00 159.24 20.76 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 5271 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.339: 1374 0.339 - 0.679: 1 0.679 - 1.018: 0 1.018 - 1.357: 0 1.357 - 1.697: 1 Chirality restraints: 1376 Sorted by residual: chirality pdb=" CG LEU A 227 " pdb=" CB LEU A 227 " pdb=" CD1 LEU A 227 " pdb=" CD2 LEU A 227 " both_signs ideal model delta sigma weight residual False -2.59 -0.89 -1.70 2.00e-01 2.50e+01 7.20e+01 chirality pdb=" CA PRO G 53 " pdb=" N PRO G 53 " pdb=" C PRO G 53 " pdb=" CB PRO G 53 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.96e+00 chirality pdb=" C2' NEC R 801 " pdb=" C1' NEC R 801 " pdb=" C3' NEC R 801 " pdb=" O2' NEC R 801 " both_signs ideal model delta sigma weight residual False -2.73 -2.49 -0.24 2.00e-01 2.50e+01 1.44e+00 ... (remaining 1373 not shown) Planarity restraints: 1499 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL R 258 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.02e+00 pdb=" N PRO R 259 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO R 259 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 259 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 277 " -0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO R 278 " 0.086 5.00e-02 4.00e+02 pdb=" CA PRO R 278 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO R 278 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 14 " 0.009 2.00e-02 2.50e+03 1.90e-02 3.62e+00 pdb=" C LEU B 14 " -0.033 2.00e-02 2.50e+03 pdb=" O LEU B 14 " 0.012 2.00e-02 2.50e+03 pdb=" N LYS B 15 " 0.011 2.00e-02 2.50e+03 ... (remaining 1496 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 122 2.64 - 3.20: 8071 3.20 - 3.77: 13311 3.77 - 4.33: 19282 4.33 - 4.90: 31789 Nonbonded interactions: 72575 Sorted by model distance: nonbonded pdb=" O ASP B 163 " pdb=" OG1 THR B 164 " model vdw 2.070 3.040 nonbonded pdb=" O THR B 86 " pdb=" OG1 THR B 87 " model vdw 2.085 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.098 3.040 nonbonded pdb=" OE2 GLU A 14 " pdb=" OG1 THR S 57 " model vdw 2.103 3.040 nonbonded pdb=" OE1 GLN S 130 " pdb=" OG1 THR S 231 " model vdw 2.121 3.040 ... (remaining 72570 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 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: 0.300 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.150 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 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:11.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6887 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 : 0.004 0.154 8879 Z= 0.221 Angle : 0.657 14.994 12027 Z= 0.361 Chirality : 0.063 1.697 1376 Planarity : 0.004 0.050 1499 Dihedral : 13.132 77.755 3199 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.02 (0.26), residues: 1085 helix: 1.45 (0.28), residues: 363 sheet: -0.82 (0.29), residues: 293 loop : -0.57 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE B 234 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.14226 ( 432) hydrogen bonds : angle 6.23325 ( 1212) SS BOND : bond 0.00490 ( 3) SS BOND : angle 1.04153 ( 6) covalent geometry : bond 0.00430 ( 8876) covalent geometry : angle 0.65646 (12021) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 0.963 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8608 (mt) cc_final: 0.8191 (mt) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.3437 time to fit residues: 321.4863 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 30 ASN R 79 HIS ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 255 ASN A 294 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.106157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082631 restraints weight = 20868.130| |-----------------------------------------------------------------------------| r_work (start): 0.3483 rms_B_bonded: 3.46 r_work: 0.3349 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.2941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 8879 Z= 0.212 Angle : 0.734 11.152 12027 Z= 0.375 Chirality : 0.046 0.233 1376 Planarity : 0.005 0.069 1499 Dihedral : 5.090 51.788 1219 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 12.80 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.00 (0.26), residues: 1085 helix: 1.38 (0.27), residues: 370 sheet: -0.66 (0.29), residues: 297 loop : -0.63 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.007 0.001 HIS A 322 PHE 0.017 0.002 PHE B 199 TYR 0.016 0.002 TYR A 302 ARG 0.007 0.001 ARG S 148 Details of bonding type rmsd hydrogen bonds : bond 0.05120 ( 432) hydrogen bonds : angle 5.30434 ( 1212) SS BOND : bond 0.00275 ( 3) SS BOND : angle 1.08305 ( 6) covalent geometry : bond 0.00498 ( 8876) covalent geometry : angle 0.73428 (12021) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 THR cc_start: 0.7588 (p) cc_final: 0.7327 (p) REVERT: A 298 GLU cc_start: 0.9212 (tp30) cc_final: 0.8798 (tt0) REVERT: B 176 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8584 (mt0) REVERT: B 226 GLU cc_start: 0.7874 (mp0) cc_final: 0.7635 (mp0) REVERT: B 259 GLN cc_start: 0.8130 (tt0) cc_final: 0.7906 (pt0) REVERT: B 336 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8604 (mp) REVERT: S 174 GLN cc_start: 0.8559 (tt0) cc_final: 0.8196 (mm-40) REVERT: S 206 ARG cc_start: 0.8707 (mmm-85) cc_final: 0.8432 (mmm-85) REVERT: S 207 LEU cc_start: 0.9347 (OUTLIER) cc_final: 0.9130 (tm) outliers start: 30 outliers final: 12 residues processed: 166 average time/residue: 1.3099 time to fit residues: 230.7205 Evaluate side-chains 131 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 116 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 74 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 7.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 322 HIS B 176 GLN B 266 HIS S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.106231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.082980 restraints weight = 21083.263| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 3.46 r_work: 0.3370 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7694 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8879 Z= 0.162 Angle : 0.675 12.517 12027 Z= 0.347 Chirality : 0.044 0.247 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.805 50.579 1219 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 3.67 % Allowed : 16.47 % Favored : 79.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.25 (0.27), residues: 1085 helix: 1.66 (0.28), residues: 364 sheet: -0.42 (0.29), residues: 288 loop : -0.63 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP R 184 HIS 0.005 0.001 HIS A 322 PHE 0.014 0.001 PHE B 253 TYR 0.015 0.001 TYR A 287 ARG 0.008 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.04676 ( 432) hydrogen bonds : angle 5.08226 ( 1212) SS BOND : bond 0.00344 ( 3) SS BOND : angle 0.75054 ( 6) covalent geometry : bond 0.00373 ( 8876) covalent geometry : angle 0.67501 (12021) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 127 time to evaluate : 0.974 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 THR cc_start: 0.7481 (p) cc_final: 0.7238 (p) REVERT: A 28 GLU cc_start: 0.7510 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: A 32 ARG cc_start: 0.7624 (ptp90) cc_final: 0.7141 (ptp90) REVERT: A 298 GLU cc_start: 0.9212 (tp30) cc_final: 0.8786 (tt0) REVERT: B 78 LYS cc_start: 0.9152 (tppp) cc_final: 0.8797 (tptm) REVERT: B 217 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5489 (pp-130) REVERT: B 226 GLU cc_start: 0.8011 (mp0) cc_final: 0.7679 (mp0) REVERT: B 259 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7981 (pt0) REVERT: S 93 MET cc_start: 0.8390 (ttt) cc_final: 0.8041 (tmt) REVERT: S 174 GLN cc_start: 0.8574 (tt0) cc_final: 0.8236 (mm-40) REVERT: S 206 ARG cc_start: 0.8764 (mmm-85) cc_final: 0.8483 (mmm-85) REVERT: S 207 LEU cc_start: 0.9296 (tm) cc_final: 0.9091 (tm) outliers start: 35 outliers final: 14 residues processed: 152 average time/residue: 1.2346 time to fit residues: 199.5900 Evaluate side-chains 136 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 119 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 85 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 40 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3920 r_free = 0.3920 target = 0.104817 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.081848 restraints weight = 21030.199| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.41 r_work: 0.3347 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 8879 Z= 0.176 Angle : 0.675 12.949 12027 Z= 0.343 Chirality : 0.044 0.257 1376 Planarity : 0.004 0.053 1499 Dihedral : 4.746 49.954 1219 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 4.09 % Allowed : 17.84 % Favored : 78.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.16 (0.27), residues: 1085 helix: 1.52 (0.28), residues: 372 sheet: -0.40 (0.30), residues: 288 loop : -0.72 (0.32), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP R 184 HIS 0.005 0.001 HIS B 225 PHE 0.013 0.001 PHE B 253 TYR 0.023 0.001 TYR A 302 ARG 0.006 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04746 ( 432) hydrogen bonds : angle 5.03786 ( 1212) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.73065 ( 6) covalent geometry : bond 0.00410 ( 8876) covalent geometry : angle 0.67524 (12021) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 129 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8448 (mt0) cc_final: 0.8102 (mt0) REVERT: R 243 LEU cc_start: 0.8816 (OUTLIER) cc_final: 0.8559 (mt) REVERT: R 290 GLU cc_start: 0.8968 (mm-30) cc_final: 0.8666 (mp0) REVERT: A 28 GLU cc_start: 0.7606 (OUTLIER) cc_final: 0.7271 (tp30) REVERT: A 32 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7519 (ptp90) REVERT: A 294 ASN cc_start: 0.8870 (OUTLIER) cc_final: 0.8526 (t0) REVERT: A 298 GLU cc_start: 0.9211 (tp30) cc_final: 0.8790 (tt0) REVERT: B 14 LEU cc_start: 0.9205 (mt) cc_final: 0.9002 (mt) REVERT: B 44 GLN cc_start: 0.8819 (OUTLIER) cc_final: 0.8377 (mt0) REVERT: B 78 LYS cc_start: 0.9172 (tppp) cc_final: 0.8871 (tptm) REVERT: B 176 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8654 (mt0) REVERT: B 211 TRP cc_start: 0.7369 (OUTLIER) cc_final: 0.7154 (m-10) REVERT: B 217 MET cc_start: 0.6517 (OUTLIER) cc_final: 0.5591 (pp-130) REVERT: B 226 GLU cc_start: 0.8064 (mp0) cc_final: 0.7667 (mp0) REVERT: G 47 GLU cc_start: 0.7376 (pm20) cc_final: 0.7173 (pm20) REVERT: S 13 GLN cc_start: 0.5952 (OUTLIER) cc_final: 0.5652 (pp30) REVERT: S 93 MET cc_start: 0.8290 (ttt) cc_final: 0.7991 (tmt) REVERT: S 148 ARG cc_start: 0.8139 (ppp80) cc_final: 0.7894 (ppp80) REVERT: S 174 GLN cc_start: 0.8580 (tt0) cc_final: 0.8228 (mm-40) REVERT: S 206 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8451 (mmm-85) REVERT: S 207 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.9036 (tm) outliers start: 39 outliers final: 17 residues processed: 160 average time/residue: 1.2797 time to fit residues: 217.5144 Evaluate side-chains 145 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 119 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 136 LEU Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.8980 chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 102 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 88 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 255 ASN ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.100728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.077565 restraints weight = 21469.177| |-----------------------------------------------------------------------------| r_work (start): 0.3407 rms_B_bonded: 3.44 r_work: 0.3263 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.4102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.130 8879 Z= 0.333 Angle : 0.791 11.654 12027 Z= 0.406 Chirality : 0.048 0.216 1376 Planarity : 0.005 0.071 1499 Dihedral : 4.997 22.033 1217 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.61 % Favored : 95.30 % Rotamer: Outliers : 5.04 % Allowed : 18.05 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.09 (0.26), residues: 1085 helix: 1.31 (0.27), residues: 365 sheet: -0.63 (0.30), residues: 283 loop : -0.74 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 184 HIS 0.010 0.002 HIS B 225 PHE 0.021 0.002 PHE B 199 TYR 0.027 0.002 TYR A 302 ARG 0.007 0.001 ARG B 137 Details of bonding type rmsd hydrogen bonds : bond 0.05790 ( 432) hydrogen bonds : angle 5.34369 ( 1212) SS BOND : bond 0.00350 ( 3) SS BOND : angle 0.98613 ( 6) covalent geometry : bond 0.00775 ( 8876) covalent geometry : angle 0.79068 (12021) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 125 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8533 (mt0) cc_final: 0.7997 (mp10) REVERT: R 90 MET cc_start: 0.7583 (mtp) cc_final: 0.7287 (mtm) REVERT: R 146 MET cc_start: 0.7510 (OUTLIER) cc_final: 0.7206 (mmm) REVERT: R 151 MET cc_start: 0.7728 (mmm) cc_final: 0.7262 (mtt) REVERT: R 171 MET cc_start: 0.8025 (tpp) cc_final: 0.7662 (tpp) REVERT: R 243 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8623 (mt) REVERT: A 28 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7211 (tp30) REVERT: A 32 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7540 (ptp90) REVERT: A 294 ASN cc_start: 0.9049 (OUTLIER) cc_final: 0.8835 (t0) REVERT: B 44 GLN cc_start: 0.8858 (OUTLIER) cc_final: 0.8387 (mt0) REVERT: B 78 LYS cc_start: 0.9123 (tppp) cc_final: 0.8834 (tptm) REVERT: B 176 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8706 (mt0) REVERT: B 211 TRP cc_start: 0.7443 (OUTLIER) cc_final: 0.5364 (m-90) REVERT: B 226 GLU cc_start: 0.8222 (mp0) cc_final: 0.7831 (mp0) REVERT: B 262 MET cc_start: 0.8166 (tpp) cc_final: 0.7659 (mmm) REVERT: G 21 MET cc_start: 0.9057 (mmm) cc_final: 0.8557 (mpm) REVERT: S 13 GLN cc_start: 0.6206 (OUTLIER) cc_final: 0.5970 (pp30) REVERT: S 83 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.7308 (mtm) REVERT: S 174 GLN cc_start: 0.8595 (tt0) cc_final: 0.8196 (mm-40) REVERT: S 207 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9102 (tm) outliers start: 48 outliers final: 19 residues processed: 159 average time/residue: 1.2530 time to fit residues: 211.3832 Evaluate side-chains 145 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 116 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 191 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 325 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 100 ILE Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 106 optimal weight: 9.9990 chunk 36 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 271 HIS A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3909 r_free = 0.3909 target = 0.104001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.080971 restraints weight = 20796.724| |-----------------------------------------------------------------------------| r_work (start): 0.3479 rms_B_bonded: 3.44 r_work: 0.3337 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.4230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8879 Z= 0.153 Angle : 0.707 12.730 12027 Z= 0.357 Chirality : 0.045 0.211 1376 Planarity : 0.004 0.053 1499 Dihedral : 4.592 21.560 1217 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 4.30 % Allowed : 20.67 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: -0.03 (0.26), residues: 1085 helix: 1.34 (0.28), residues: 376 sheet: -0.52 (0.30), residues: 282 loop : -0.81 (0.31), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP R 184 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE B 253 TYR 0.022 0.001 TYR A 302 ARG 0.009 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.04728 ( 432) hydrogen bonds : angle 5.04998 ( 1212) SS BOND : bond 0.00361 ( 3) SS BOND : angle 0.61653 ( 6) covalent geometry : bond 0.00351 ( 8876) covalent geometry : angle 0.70728 (12021) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 124 time to evaluate : 0.987 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 44 GLN cc_start: 0.8453 (mt0) cc_final: 0.8127 (mt0) REVERT: R 192 MET cc_start: 0.7448 (mtm) cc_final: 0.7217 (mtp) REVERT: R 243 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 28 GLU cc_start: 0.7454 (OUTLIER) cc_final: 0.7216 (tm-30) REVERT: A 32 ARG cc_start: 0.7747 (ptp90) cc_final: 0.7409 (mtm110) REVERT: A 208 ARG cc_start: 0.6035 (mmm-85) cc_final: 0.5633 (tpt90) REVERT: A 294 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8543 (t0) REVERT: B 78 LYS cc_start: 0.9137 (tppp) cc_final: 0.8862 (tptm) REVERT: B 176 GLN cc_start: 0.9159 (OUTLIER) cc_final: 0.8636 (mt0) REVERT: B 211 TRP cc_start: 0.7254 (OUTLIER) cc_final: 0.5237 (m-90) REVERT: B 217 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.5590 (pp-130) REVERT: B 226 GLU cc_start: 0.8359 (mp0) cc_final: 0.7972 (mp0) REVERT: B 262 MET cc_start: 0.8008 (tpp) cc_final: 0.7585 (mmm) REVERT: S 13 GLN cc_start: 0.6307 (OUTLIER) cc_final: 0.6062 (pp30) REVERT: S 174 GLN cc_start: 0.8560 (tt0) cc_final: 0.8155 (mm-40) REVERT: S 207 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9138 (tm) outliers start: 41 outliers final: 11 residues processed: 158 average time/residue: 1.2599 time to fit residues: 211.4037 Evaluate side-chains 138 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 119 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 81 optimal weight: 0.0980 chunk 64 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 76 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.104913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082117 restraints weight = 21098.033| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.46 r_work: 0.3362 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.4348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8879 Z= 0.142 Angle : 0.728 13.472 12027 Z= 0.363 Chirality : 0.044 0.201 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.437 20.965 1217 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.32 % Favored : 96.59 % Rotamer: Outliers : 3.57 % Allowed : 22.14 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.06 (0.26), residues: 1085 helix: 1.47 (0.28), residues: 379 sheet: -0.44 (0.31), residues: 280 loop : -0.85 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP R 184 HIS 0.009 0.001 HIS R 271 PHE 0.026 0.001 PHE R 48 TYR 0.017 0.001 TYR B 59 ARG 0.008 0.001 ARG S 18 Details of bonding type rmsd hydrogen bonds : bond 0.04566 ( 432) hydrogen bonds : angle 4.95810 ( 1212) SS BOND : bond 0.00378 ( 3) SS BOND : angle 0.50063 ( 6) covalent geometry : bond 0.00320 ( 8876) covalent geometry : angle 0.72777 (12021) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 0.934 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ASN cc_start: 0.8405 (t0) cc_final: 0.7777 (t0) REVERT: R 44 GLN cc_start: 0.8290 (mt0) cc_final: 0.7889 (mp10) REVERT: R 151 MET cc_start: 0.7586 (mmm) cc_final: 0.7063 (mtp) REVERT: R 171 MET cc_start: 0.7871 (tpp) cc_final: 0.7570 (tpp) REVERT: R 192 MET cc_start: 0.7418 (mtm) cc_final: 0.7203 (mtp) REVERT: R 243 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8390 (mt) REVERT: R 275 MET cc_start: 0.8300 (pp-130) cc_final: 0.8074 (pp-130) REVERT: R 290 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8650 (mp0) REVERT: A 28 GLU cc_start: 0.7406 (OUTLIER) cc_final: 0.7204 (tm-30) REVERT: A 32 ARG cc_start: 0.7673 (ptp90) cc_final: 0.7411 (mtm110) REVERT: A 294 ASN cc_start: 0.8881 (m-40) cc_final: 0.8405 (t0) REVERT: B 78 LYS cc_start: 0.9092 (tppp) cc_final: 0.8834 (tptm) REVERT: B 176 GLN cc_start: 0.9154 (OUTLIER) cc_final: 0.8604 (mt0) REVERT: B 211 TRP cc_start: 0.7331 (OUTLIER) cc_final: 0.4961 (m-90) REVERT: B 217 MET cc_start: 0.6542 (OUTLIER) cc_final: 0.5630 (pp-130) REVERT: B 226 GLU cc_start: 0.8439 (mp0) cc_final: 0.8032 (mp0) REVERT: G 15 LEU cc_start: 0.9429 (tm) cc_final: 0.9172 (mp) REVERT: G 47 GLU cc_start: 0.7630 (pm20) cc_final: 0.7370 (pm20) REVERT: S 13 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.6058 (pp30) REVERT: S 162 LEU cc_start: 0.8007 (OUTLIER) cc_final: 0.7777 (tp) REVERT: S 174 GLN cc_start: 0.8575 (tt0) cc_final: 0.8154 (mm-40) REVERT: S 206 ARG cc_start: 0.8823 (mpp-170) cc_final: 0.8138 (mpp-170) REVERT: S 207 LEU cc_start: 0.9396 (tm) cc_final: 0.8982 (tm) outliers start: 34 outliers final: 15 residues processed: 158 average time/residue: 1.2493 time to fit residues: 209.9508 Evaluate side-chains 138 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 116 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 29 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 13 optimal weight: 4.9990 chunk 72 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.104941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082076 restraints weight = 20992.232| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.43 r_work: 0.3364 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 moved from start: 0.4458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 8879 Z= 0.152 Angle : 0.765 13.827 12027 Z= 0.377 Chirality : 0.045 0.227 1376 Planarity : 0.005 0.054 1499 Dihedral : 4.454 20.353 1217 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.36 % Allowed : 23.71 % Favored : 72.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.01 (0.26), residues: 1085 helix: 1.41 (0.28), residues: 381 sheet: -0.43 (0.31), residues: 280 loop : -0.91 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP R 184 HIS 0.009 0.001 HIS R 271 PHE 0.013 0.001 PHE B 253 TYR 0.014 0.001 TYR A 302 ARG 0.009 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04621 ( 432) hydrogen bonds : angle 4.97224 ( 1212) SS BOND : bond 0.00337 ( 3) SS BOND : angle 0.53369 ( 6) covalent geometry : bond 0.00350 ( 8876) covalent geometry : angle 0.76483 (12021) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 124 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ASN cc_start: 0.8417 (t0) cc_final: 0.7815 (t0) REVERT: R 44 GLN cc_start: 0.8265 (mt0) cc_final: 0.7881 (mp10) REVERT: R 151 MET cc_start: 0.7586 (mmm) cc_final: 0.7049 (mtp) REVERT: R 171 MET cc_start: 0.7933 (tpp) cc_final: 0.7686 (tpp) REVERT: R 243 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8392 (mt) REVERT: R 290 GLU cc_start: 0.8912 (mm-30) cc_final: 0.8656 (mp0) REVERT: A 28 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7189 (tm-30) REVERT: A 32 ARG cc_start: 0.7789 (ptp90) cc_final: 0.7452 (mtm110) REVERT: A 205 ARG cc_start: 0.7756 (pmt-80) cc_final: 0.7490 (pmt-80) REVERT: A 208 ARG cc_start: 0.6085 (mmm-85) cc_final: 0.5694 (tpt90) REVERT: A 294 ASN cc_start: 0.8839 (m-40) cc_final: 0.8321 (t0) REVERT: B 78 LYS cc_start: 0.9096 (tppp) cc_final: 0.8834 (tptm) REVERT: B 176 GLN cc_start: 0.9130 (OUTLIER) cc_final: 0.8594 (mt0) REVERT: B 217 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5631 (pp-130) REVERT: B 226 GLU cc_start: 0.8475 (mp0) cc_final: 0.8061 (mp0) REVERT: B 262 MET cc_start: 0.7973 (tpp) cc_final: 0.7254 (mmp) REVERT: G 15 LEU cc_start: 0.9388 (tm) cc_final: 0.9057 (mp) REVERT: G 20 LYS cc_start: 0.9569 (pptt) cc_final: 0.9364 (pptt) REVERT: S 13 GLN cc_start: 0.6315 (OUTLIER) cc_final: 0.6073 (pp30) REVERT: S 73 ASP cc_start: 0.7068 (t0) cc_final: 0.6682 (t0) REVERT: S 162 LEU cc_start: 0.7990 (OUTLIER) cc_final: 0.7770 (tp) REVERT: S 174 GLN cc_start: 0.8583 (tt0) cc_final: 0.8151 (mm-40) REVERT: S 206 ARG cc_start: 0.8512 (mpp-170) cc_final: 0.8292 (mpp-170) REVERT: S 207 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.8964 (tm) outliers start: 32 outliers final: 15 residues processed: 149 average time/residue: 1.2478 time to fit residues: 197.7868 Evaluate side-chains 141 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 207 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 73 optimal weight: 5.9990 chunk 104 optimal weight: 0.0970 chunk 13 optimal weight: 0.0980 chunk 96 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.105801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.083035 restraints weight = 20990.646| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.45 r_work: 0.3382 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.4559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8879 Z= 0.147 Angle : 0.808 15.213 12027 Z= 0.395 Chirality : 0.045 0.225 1376 Planarity : 0.005 0.052 1499 Dihedral : 4.358 20.126 1217 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.15 % Allowed : 24.34 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.07 (0.26), residues: 1085 helix: 1.45 (0.28), residues: 382 sheet: -0.38 (0.31), residues: 280 loop : -0.87 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP R 184 HIS 0.008 0.001 HIS R 271 PHE 0.014 0.001 PHE B 253 TYR 0.014 0.001 TYR A 287 ARG 0.010 0.001 ARG A 24 Details of bonding type rmsd hydrogen bonds : bond 0.04649 ( 432) hydrogen bonds : angle 4.94767 ( 1212) SS BOND : bond 0.00410 ( 3) SS BOND : angle 0.47250 ( 6) covalent geometry : bond 0.00337 ( 8876) covalent geometry : angle 0.80793 (12021) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 131 time to evaluate : 0.901 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 151 MET cc_start: 0.7480 (mmm) cc_final: 0.6973 (mtp) REVERT: R 171 MET cc_start: 0.7878 (tpp) cc_final: 0.7539 (tpp) REVERT: R 192 MET cc_start: 0.7360 (mtm) cc_final: 0.7111 (mtp) REVERT: R 243 LEU cc_start: 0.8632 (OUTLIER) cc_final: 0.8341 (mt) REVERT: A 32 ARG cc_start: 0.7763 (ptp90) cc_final: 0.7515 (mtm110) REVERT: A 208 ARG cc_start: 0.5925 (mmm-85) cc_final: 0.5572 (tpt90) REVERT: A 294 ASN cc_start: 0.8796 (m-40) cc_final: 0.8244 (t0) REVERT: B 176 GLN cc_start: 0.9116 (OUTLIER) cc_final: 0.8586 (mt0) REVERT: B 217 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5611 (pp-130) REVERT: B 226 GLU cc_start: 0.8491 (mp0) cc_final: 0.8044 (mp0) REVERT: B 262 MET cc_start: 0.8052 (tpp) cc_final: 0.7320 (mmp) REVERT: B 294 CYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8045 (m) REVERT: G 15 LEU cc_start: 0.9279 (tm) cc_final: 0.8919 (mp) REVERT: G 20 LYS cc_start: 0.9531 (pptt) cc_final: 0.9321 (pptt) REVERT: G 21 MET cc_start: 0.8737 (mmm) cc_final: 0.8391 (mmm) REVERT: S 13 GLN cc_start: 0.6321 (OUTLIER) cc_final: 0.6067 (pp30) REVERT: S 73 ASP cc_start: 0.7075 (t0) cc_final: 0.6679 (t70) REVERT: S 162 LEU cc_start: 0.8024 (OUTLIER) cc_final: 0.7796 (tp) REVERT: S 174 GLN cc_start: 0.8564 (tt0) cc_final: 0.8168 (mm-40) outliers start: 30 outliers final: 16 residues processed: 153 average time/residue: 1.2819 time to fit residues: 208.0901 Evaluate side-chains 137 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 115 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 43 LEU Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain A residue 287 TYR Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 225 HIS Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 0.0050 chunk 27 optimal weight: 0.8980 chunk 69 optimal weight: 8.9990 chunk 91 optimal weight: 0.0030 chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 10.0000 chunk 76 optimal weight: 0.0980 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 overall best weight: 0.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 204 GLN A 244 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.107379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.084849 restraints weight = 20904.388| |-----------------------------------------------------------------------------| r_work (start): 0.3559 rms_B_bonded: 3.47 r_work: 0.3417 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 8879 Z= 0.145 Angle : 0.840 14.598 12027 Z= 0.408 Chirality : 0.046 0.252 1376 Planarity : 0.005 0.056 1499 Dihedral : 4.316 21.844 1217 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.10 % Allowed : 26.02 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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 (0.26), residues: 1085 helix: 1.41 (0.28), residues: 382 sheet: -0.36 (0.31), residues: 280 loop : -0.93 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.050 0.001 TRP R 184 HIS 0.007 0.001 HIS R 271 PHE 0.013 0.001 PHE B 253 TYR 0.047 0.001 TYR A 302 ARG 0.017 0.001 ARG S 206 Details of bonding type rmsd hydrogen bonds : bond 0.04519 ( 432) hydrogen bonds : angle 4.93061 ( 1212) SS BOND : bond 0.00423 ( 3) SS BOND : angle 0.49867 ( 6) covalent geometry : bond 0.00330 ( 8876) covalent geometry : angle 0.84036 (12021) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 132 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 63 VAL cc_start: 0.9494 (p) cc_final: 0.9261 (m) REVERT: R 151 MET cc_start: 0.7558 (mmm) cc_final: 0.7131 (mtt) REVERT: R 171 MET cc_start: 0.7821 (tpp) cc_final: 0.7495 (tpp) REVERT: R 192 MET cc_start: 0.7372 (mtm) cc_final: 0.7136 (mtp) REVERT: R 243 LEU cc_start: 0.8664 (OUTLIER) cc_final: 0.8380 (mt) REVERT: R 290 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8669 (mp0) REVERT: A 208 ARG cc_start: 0.5911 (mmm-85) cc_final: 0.5475 (tpt90) REVERT: A 294 ASN cc_start: 0.8732 (m-40) cc_final: 0.8171 (t0) REVERT: A 350 ASP cc_start: 0.8051 (OUTLIER) cc_final: 0.7565 (m-30) REVERT: B 217 MET cc_start: 0.6472 (OUTLIER) cc_final: 0.5540 (pp-130) REVERT: B 226 GLU cc_start: 0.8498 (mp0) cc_final: 0.8068 (mp0) REVERT: B 294 CYS cc_start: 0.8471 (OUTLIER) cc_final: 0.7997 (m) REVERT: G 15 LEU cc_start: 0.9303 (tm) cc_final: 0.8942 (mt) REVERT: G 17 GLU cc_start: 0.9353 (tp30) cc_final: 0.9074 (tp30) REVERT: G 21 MET cc_start: 0.8797 (mmm) cc_final: 0.8234 (mmt) REVERT: G 47 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8236 (pm20) REVERT: S 13 GLN cc_start: 0.6263 (OUTLIER) cc_final: 0.6015 (pp30) REVERT: S 73 ASP cc_start: 0.7020 (t0) cc_final: 0.6604 (t70) REVERT: S 162 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7782 (tp) REVERT: S 174 GLN cc_start: 0.8555 (tt0) cc_final: 0.8148 (mm-40) REVERT: S 208 GLU cc_start: 0.8749 (pp20) cc_final: 0.8330 (pp20) outliers start: 20 outliers final: 9 residues processed: 148 average time/residue: 1.2381 time to fit residues: 194.8970 Evaluate side-chains 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 350 ASP Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 0.3980 chunk 7 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 12 optimal weight: 0.9980 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 81 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN A 244 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.106808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.084092 restraints weight = 20963.895| |-----------------------------------------------------------------------------| r_work (start): 0.3543 rms_B_bonded: 3.46 r_work: 0.3405 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.4742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 8879 Z= 0.149 Angle : 0.835 14.507 12027 Z= 0.407 Chirality : 0.045 0.222 1376 Planarity : 0.005 0.051 1499 Dihedral : 4.307 20.866 1217 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.52 % Allowed : 26.13 % Favored : 71.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % 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: 0.01 (0.26), residues: 1085 helix: 1.38 (0.28), residues: 382 sheet: -0.35 (0.31), residues: 280 loop : -0.95 (0.31), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.001 TRP R 184 HIS 0.008 0.001 HIS R 271 PHE 0.029 0.001 PHE R 48 TYR 0.010 0.001 TYR S 178 ARG 0.008 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04535 ( 432) hydrogen bonds : angle 4.93706 ( 1212) SS BOND : bond 0.00330 ( 3) SS BOND : angle 0.48034 ( 6) covalent geometry : bond 0.00346 ( 8876) covalent geometry : angle 0.83559 (12021) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7646.97 seconds wall clock time: 131 minutes 19.62 seconds (7879.62 seconds total)