Starting phenix.real_space_refine on Wed Sep 17 12:08:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh0_39278/09_2025/8yh0_39278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh0_39278/09_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_39278/09_2025/8yh0_39278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh0_39278/09_2025/8yh0_39278.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh0_39278/09_2025/8yh0_39278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh0_39278/09_2025/8yh0_39278.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.12, per 1000 atoms: 0.24 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: 0.89 Conformation dependent library (CDL) restraints added in 320.9 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.28 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: 1.11 Time building geometry restraints manager: 1.11 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: 0.520 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.750 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.440 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (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 ARG 0.003 0.000 ARG B 314 TYR 0.012 0.001 TYR S 178 PHE 0.018 0.001 PHE B 234 TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 Details of bonding type rmsd covalent geometry : bond 0.00430 ( 8876) covalent geometry : angle 0.65646 (12021) SS BOND : bond 0.00490 ( 3) SS BOND : angle 1.04153 ( 6) hydrogen bonds : bond 0.14226 ( 432) hydrogen bonds : angle 6.23325 ( 1212) *********************** 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 : 0.348 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: 0.6270 time to fit residues: 149.4691 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 : 0.346 ------------------------------------------------------------------------------- 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 108 optimal weight: 6.9990 chunk 49 optimal weight: 20.0000 chunk 97 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 79 HIS ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 174 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.103773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.080273 restraints weight = 21302.975| |-----------------------------------------------------------------------------| r_work (start): 0.3435 rms_B_bonded: 3.46 r_work: 0.3299 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3299 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.116 8879 Z= 0.295 Angle : 0.791 11.703 12027 Z= 0.408 Chirality : 0.048 0.234 1376 Planarity : 0.006 0.069 1499 Dihedral : 5.296 52.302 1219 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 12.10 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.50 % Favored : 96.41 % Rotamer: Outliers : 3.88 % Allowed : 12.91 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.21 (0.26), residues: 1085 helix: 1.17 (0.27), residues: 369 sheet: -0.84 (0.28), residues: 298 loop : -0.65 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 137 TYR 0.023 0.002 TYR A 302 PHE 0.020 0.002 PHE B 199 TRP 0.019 0.002 TRP R 184 HIS 0.009 0.002 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00689 ( 8876) covalent geometry : angle 0.79103 (12021) SS BOND : bond 0.00351 ( 3) SS BOND : angle 1.35746 ( 6) hydrogen bonds : bond 0.05659 ( 432) hydrogen bonds : angle 5.46767 ( 1212) *********************** 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 180 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 143 time to evaluate : 0.325 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: 0.7634 (p) cc_final: 0.7396 (p) REVERT: R 251 ILE cc_start: 0.8718 (OUTLIER) cc_final: 0.8439 (mp) REVERT: A 28 GLU cc_start: 0.7505 (OUTLIER) cc_final: 0.7164 (tp30) REVERT: A 32 ARG cc_start: 0.7744 (ptp90) cc_final: 0.7267 (ptp90) REVERT: A 276 GLU cc_start: 0.8979 (mp0) cc_final: 0.8642 (mp0) REVERT: A 298 GLU cc_start: 0.9252 (tp30) cc_final: 0.8799 (tt0) REVERT: B 176 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8660 (mt0) REVERT: B 226 GLU cc_start: 0.7897 (mp0) cc_final: 0.7624 (mp0) REVERT: B 259 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7908 (pt0) REVERT: S 174 GLN cc_start: 0.8588 (tt0) cc_final: 0.8152 (mm-40) REVERT: S 206 ARG cc_start: 0.8729 (mmm-85) cc_final: 0.8430 (mmm-85) REVERT: S 207 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.9129 (tm) outliers start: 37 outliers final: 16 residues processed: 166 average time/residue: 0.6082 time to fit residues: 106.9862 Evaluate side-chains 140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 141 VAL 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 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 332 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 259 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 Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 93 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 71 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 103 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 A 322 HIS B 176 GLN B 266 HIS B 295 ASN S 130 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.106150 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.082747 restraints weight = 21253.653| |-----------------------------------------------------------------------------| r_work (start): 0.3488 rms_B_bonded: 3.51 r_work: 0.3357 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.3422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8879 Z= 0.144 Angle : 0.671 12.518 12027 Z= 0.344 Chirality : 0.044 0.255 1376 Planarity : 0.005 0.057 1499 Dihedral : 4.804 51.170 1219 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.09 % Allowed : 2.95 % Favored : 96.96 % Rotamer: Outliers : 3.99 % Allowed : 16.05 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.26), residues: 1085 helix: 1.28 (0.28), residues: 383 sheet: -0.52 (0.29), residues: 284 loop : -0.69 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 13 TYR 0.019 0.001 TYR A 287 PHE 0.015 0.001 PHE B 253 TRP 0.029 0.001 TRP R 184 HIS 0.005 0.001 HIS A 322 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 8876) covalent geometry : angle 0.67113 (12021) SS BOND : bond 0.00345 ( 3) SS BOND : angle 0.69208 ( 6) hydrogen bonds : bond 0.04620 ( 432) hydrogen bonds : angle 5.08691 ( 1212) *********************** 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 172 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 134 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 58 ASP cc_start: 0.8950 (m-30) cc_final: 0.8713 (m-30) REVERT: A 28 GLU cc_start: 0.7409 (OUTLIER) cc_final: 0.7097 (tp30) REVERT: A 32 ARG cc_start: 0.7580 (ptp90) cc_final: 0.7033 (ptp90) REVERT: A 276 GLU cc_start: 0.8964 (mp0) cc_final: 0.8647 (mp0) REVERT: A 294 ASN cc_start: 0.8888 (m-40) cc_final: 0.8574 (t0) REVERT: A 298 GLU cc_start: 0.9159 (tp30) cc_final: 0.8714 (tt0) REVERT: B 78 LYS cc_start: 0.9107 (tppp) cc_final: 0.8761 (tptm) REVERT: B 211 TRP cc_start: 0.7257 (OUTLIER) cc_final: 0.7037 (m-10) REVERT: B 217 MET cc_start: 0.6415 (OUTLIER) cc_final: 0.5557 (pp-130) REVERT: B 226 GLU cc_start: 0.8073 (mp0) cc_final: 0.7694 (mp0) REVERT: G 41 CYS cc_start: 0.5872 (OUTLIER) cc_final: 0.5496 (m) REVERT: S 83 MET cc_start: 0.7595 (mtm) cc_final: 0.7191 (mtm) REVERT: S 93 MET cc_start: 0.8407 (ttt) cc_final: 0.8099 (tmt) REVERT: S 174 GLN cc_start: 0.8551 (tt0) cc_final: 0.8127 (mm-40) REVERT: S 206 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8498 (mmm-85) REVERT: S 207 LEU cc_start: 0.9289 (tm) cc_final: 0.9078 (tm) outliers start: 38 outliers final: 11 residues processed: 161 average time/residue: 0.5982 time to fit residues: 102.0528 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 : 0.258 ------------------------------------------------------------------------------- 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 247 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 172 GLU Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 145 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 60 optimal weight: 2.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 51 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 103 optimal weight: 9.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 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 = 0.3922 r_free = 0.3922 target = 0.105229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081980 restraints weight = 21572.109| |-----------------------------------------------------------------------------| r_work (start): 0.3477 rms_B_bonded: 3.53 r_work: 0.3344 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3344 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7670 moved from start: 0.3687 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= 0.161 Angle : 0.681 12.953 12027 Z= 0.345 Chirality : 0.044 0.227 1376 Planarity : 0.004 0.053 1499 Dihedral : 4.723 50.258 1219 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 3.57 % Allowed : 18.47 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.27), residues: 1085 helix: 1.34 (0.28), residues: 383 sheet: -0.42 (0.30), residues: 284 loop : -0.69 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.023 0.001 TYR A 302 PHE 0.014 0.001 PHE B 199 TRP 0.031 0.001 TRP R 184 HIS 0.004 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00373 ( 8876) covalent geometry : angle 0.68071 (12021) SS BOND : bond 0.00325 ( 3) SS BOND : angle 0.64554 ( 6) hydrogen bonds : bond 0.04650 ( 432) hydrogen bonds : angle 5.03007 ( 1212) *********************** 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 164 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 130 time to evaluate : 0.368 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 THR cc_start: 0.7506 (p) cc_final: 0.7258 (p) REVERT: R 243 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8485 (mt) REVERT: R 290 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8665 (mp0) REVERT: A 28 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7103 (tp30) REVERT: A 32 ARG cc_start: 0.7607 (ptp90) cc_final: 0.7154 (ptp90) REVERT: A 276 GLU cc_start: 0.8982 (mp0) cc_final: 0.8669 (mp0) REVERT: A 294 ASN cc_start: 0.8869 (m-40) cc_final: 0.8503 (t0) REVERT: A 298 GLU cc_start: 0.9129 (tp30) cc_final: 0.8686 (tt0) REVERT: B 78 LYS cc_start: 0.9128 (tppp) cc_final: 0.8830 (tptm) REVERT: B 176 GLN cc_start: 0.9206 (OUTLIER) cc_final: 0.8662 (mt0) REVERT: B 211 TRP cc_start: 0.7348 (OUTLIER) cc_final: 0.7144 (m-10) REVERT: B 217 MET cc_start: 0.6420 (OUTLIER) cc_final: 0.5516 (pp-130) REVERT: B 226 GLU cc_start: 0.8081 (mp0) cc_final: 0.7665 (mp0) REVERT: B 259 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.8024 (pt0) REVERT: G 41 CYS cc_start: 0.6202 (OUTLIER) cc_final: 0.5409 (m) REVERT: G 47 GLU cc_start: 0.7431 (pm20) cc_final: 0.7207 (pm20) REVERT: S 13 GLN cc_start: 0.5847 (OUTLIER) cc_final: 0.5583 (pp30) REVERT: S 83 MET cc_start: 0.7631 (mtm) cc_final: 0.7229 (mtm) REVERT: S 87 ARG cc_start: 0.7974 (ptp-170) cc_final: 0.7698 (ptp-170) REVERT: S 93 MET cc_start: 0.8404 (ttt) cc_final: 0.8048 (tmt) REVERT: S 148 ARG cc_start: 0.8133 (ppp80) cc_final: 0.7885 (ppp80) REVERT: S 174 GLN cc_start: 0.8560 (tt0) cc_final: 0.8121 (mm-40) REVERT: S 206 ARG cc_start: 0.8859 (mmm-85) cc_final: 0.8481 (mmm-85) REVERT: S 207 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9034 (tm) outliers start: 34 outliers final: 15 residues processed: 158 average time/residue: 0.6492 time to fit residues: 108.5748 Evaluate side-chains 142 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 0.390 ------------------------------------------------------------------------------- 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 136 LEU 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 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS 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 79 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 19 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 56 optimal weight: 0.6980 chunk 47 optimal weight: 5.9990 chunk 96 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 50 optimal weight: 8.9990 chunk 100 optimal weight: 8.9990 overall best weight: 1.6384 ------------------------------------------------------------------------------- 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 269 ASN ** A 306 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 = 0.3917 r_free = 0.3917 target = 0.104870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.081488 restraints weight = 21476.695| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 3.58 r_work: 0.3338 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8879 Z= 0.164 Angle : 0.689 12.272 12027 Z= 0.348 Chirality : 0.044 0.243 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.650 50.338 1219 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 5.04 % Allowed : 18.57 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.26), residues: 1085 helix: 1.26 (0.28), residues: 390 sheet: -0.38 (0.30), residues: 284 loop : -0.76 (0.32), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.026 0.001 TYR A 302 PHE 0.013 0.001 PHE B 253 TRP 0.032 0.001 TRP R 184 HIS 0.006 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 8876) covalent geometry : angle 0.68888 (12021) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.64579 ( 6) hydrogen bonds : bond 0.04615 ( 432) hydrogen bonds : angle 5.00025 ( 1212) *********************** 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 176 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 128 time to evaluate : 0.353 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 44 GLN cc_start: 0.8340 (mt0) cc_final: 0.7963 (mt0) REVERT: R 94 THR cc_start: 0.7452 (p) cc_final: 0.7208 (p) REVERT: R 286 LYS cc_start: 0.9220 (mppt) cc_final: 0.8748 (mppt) REVERT: R 290 GLU cc_start: 0.9045 (mm-30) cc_final: 0.8738 (mp0) REVERT: A 28 GLU cc_start: 0.7312 (OUTLIER) cc_final: 0.7022 (tp30) REVERT: A 32 ARG cc_start: 0.7597 (ptp90) cc_final: 0.6928 (ptp90) REVERT: A 53 MET cc_start: 0.7789 (mtm) cc_final: 0.7476 (mtm) REVERT: A 276 GLU cc_start: 0.8977 (mp0) cc_final: 0.8653 (mp0) REVERT: A 294 ASN cc_start: 0.8835 (OUTLIER) cc_final: 0.8455 (t0) REVERT: A 298 GLU cc_start: 0.9130 (tp30) cc_final: 0.8655 (tt0) REVERT: B 44 GLN cc_start: 0.8877 (OUTLIER) cc_final: 0.8372 (mt0) REVERT: B 78 LYS cc_start: 0.9065 (tppp) cc_final: 0.8774 (tptm) REVERT: B 176 GLN cc_start: 0.9194 (OUTLIER) cc_final: 0.8650 (mt0) REVERT: B 211 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.4550 (m-10) REVERT: B 217 MET cc_start: 0.6400 (OUTLIER) cc_final: 0.5533 (pp-130) REVERT: B 226 GLU cc_start: 0.8190 (mp0) cc_final: 0.7795 (mp0) REVERT: B 259 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8077 (pt0) REVERT: B 262 MET cc_start: 0.8093 (tpp) cc_final: 0.7624 (mmm) REVERT: G 17 GLU cc_start: 0.9610 (OUTLIER) cc_final: 0.8979 (tp30) REVERT: G 21 MET cc_start: 0.8969 (mmm) cc_final: 0.8728 (mmm) REVERT: G 41 CYS cc_start: 0.5995 (OUTLIER) cc_final: 0.5388 (m) REVERT: S 13 GLN cc_start: 0.5883 (OUTLIER) cc_final: 0.5617 (pp30) REVERT: S 83 MET cc_start: 0.7639 (mtm) cc_final: 0.7268 (mtm) REVERT: S 87 ARG cc_start: 0.8021 (ptp-170) cc_final: 0.7709 (ptp-170) REVERT: S 93 MET cc_start: 0.8363 (ttt) cc_final: 0.7950 (tmt) REVERT: S 148 ARG cc_start: 0.8252 (ppp80) cc_final: 0.7995 (ppp80) REVERT: S 174 GLN cc_start: 0.8576 (tt0) cc_final: 0.8096 (mm-40) REVERT: S 207 LEU cc_start: 0.9286 (OUTLIER) cc_final: 0.9058 (tm) outliers start: 48 outliers final: 17 residues processed: 164 average time/residue: 0.6343 time to fit residues: 110.2675 Evaluate side-chains 150 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 122 time to evaluate : 0.344 ------------------------------------------------------------------------------- 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 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 41 CYS 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 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 20 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 72 optimal weight: 0.6980 chunk 78 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 52 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 = 0.3929 r_free = 0.3929 target = 0.105098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.082338 restraints weight = 21440.578| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.49 r_work: 0.3359 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8879 Z= 0.146 Angle : 0.683 12.717 12027 Z= 0.340 Chirality : 0.044 0.199 1376 Planarity : 0.004 0.051 1499 Dihedral : 4.293 20.565 1217 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 4.30 % Allowed : 20.25 % Favored : 75.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.12 (0.27), residues: 1085 helix: 1.35 (0.28), residues: 389 sheet: -0.34 (0.31), residues: 278 loop : -0.74 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.021 0.001 TYR A 302 PHE 0.013 0.001 PHE B 253 TRP 0.036 0.001 TRP R 184 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8876) covalent geometry : angle 0.68308 (12021) SS BOND : bond 0.00317 ( 3) SS BOND : angle 0.53858 ( 6) hydrogen bonds : bond 0.04459 ( 432) hydrogen bonds : angle 4.94992 ( 1212) *********************** 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 174 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 133 time to evaluate : 0.361 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: 0.8294 (mt0) cc_final: 0.7942 (mt0) REVERT: R 94 THR cc_start: 0.7468 (p) cc_final: 0.7236 (p) REVERT: R 243 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (mt) REVERT: A 28 GLU cc_start: 0.7356 (OUTLIER) cc_final: 0.7058 (tp30) REVERT: A 32 ARG cc_start: 0.7612 (ptp90) cc_final: 0.7132 (ptp90) REVERT: A 53 MET cc_start: 0.7999 (mtm) cc_final: 0.7772 (mtm) REVERT: A 205 ARG cc_start: 0.7703 (pmt170) cc_final: 0.7405 (ppt90) REVERT: A 276 GLU cc_start: 0.9002 (mp0) cc_final: 0.8655 (mp0) REVERT: A 294 ASN cc_start: 0.8796 (OUTLIER) cc_final: 0.8362 (t0) REVERT: A 298 GLU cc_start: 0.9237 (tp30) cc_final: 0.8766 (tt0) REVERT: B 44 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8399 (mt0) REVERT: B 78 LYS cc_start: 0.9110 (tppp) cc_final: 0.8826 (tptm) REVERT: B 176 GLN cc_start: 0.9195 (OUTLIER) cc_final: 0.8682 (mt0) REVERT: B 211 TRP cc_start: 0.7329 (OUTLIER) cc_final: 0.4493 (m-10) REVERT: B 217 MET cc_start: 0.6583 (OUTLIER) cc_final: 0.5662 (pp-130) REVERT: B 226 GLU cc_start: 0.8373 (mp0) cc_final: 0.7949 (mp0) REVERT: B 259 GLN cc_start: 0.8436 (OUTLIER) cc_final: 0.8095 (pt0) REVERT: B 262 MET cc_start: 0.8062 (tpp) cc_final: 0.7722 (mmm) REVERT: B 336 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8884 (tp) REVERT: G 21 MET cc_start: 0.8974 (mmm) cc_final: 0.8758 (mmm) REVERT: G 41 CYS cc_start: 0.6850 (OUTLIER) cc_final: 0.6211 (m) REVERT: S 13 GLN cc_start: 0.6134 (OUTLIER) cc_final: 0.5874 (pp30) REVERT: S 83 MET cc_start: 0.7568 (mtm) cc_final: 0.7255 (mtm) REVERT: S 87 ARG cc_start: 0.8041 (ptp-170) cc_final: 0.7724 (ptp-170) REVERT: S 93 MET cc_start: 0.8348 (ttt) cc_final: 0.8124 (ttt) REVERT: S 148 ARG cc_start: 0.8281 (ppp80) cc_final: 0.8066 (ppp80) REVERT: S 174 GLN cc_start: 0.8577 (tt0) cc_final: 0.8140 (mm-40) REVERT: S 207 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9073 (tm) outliers start: 41 outliers final: 14 residues processed: 164 average time/residue: 0.6336 time to fit residues: 110.0279 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 : 0.339 ------------------------------------------------------------------------------- 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 195 ILE 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 52 GLN Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 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 217 MET Chi-restraints excluded: chain B residue 259 GLN 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 41 CYS 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 13 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 98 optimal weight: 6.9990 chunk 93 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.0970 chunk 54 optimal weight: 4.9990 chunk 78 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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** A 22 ASN A 244 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** 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 = 0.3937 r_free = 0.3937 target = 0.105504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.082754 restraints weight = 21466.548| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 3.51 r_work: 0.3370 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8879 Z= 0.146 Angle : 0.711 13.275 12027 Z= 0.354 Chirality : 0.044 0.235 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.247 20.246 1217 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 3.99 % Allowed : 21.72 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.14 (0.27), residues: 1085 helix: 1.36 (0.28), residues: 389 sheet: -0.33 (0.31), residues: 278 loop : -0.72 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 24 TYR 0.015 0.001 TYR A 302 PHE 0.027 0.001 PHE R 48 TRP 0.037 0.001 TRP R 184 HIS 0.011 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 8876) covalent geometry : angle 0.71138 (12021) SS BOND : bond 0.00341 ( 3) SS BOND : angle 0.49131 ( 6) hydrogen bonds : bond 0.04408 ( 432) hydrogen bonds : angle 4.95096 ( 1212) *********************** 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 161 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ASN cc_start: 0.8480 (t0) cc_final: 0.8246 (t0) REVERT: R 44 GLN cc_start: 0.8281 (mt0) cc_final: 0.7941 (mt0) REVERT: R 94 THR cc_start: 0.7503 (p) cc_final: 0.7268 (p) REVERT: R 151 MET cc_start: 0.7500 (mmm) cc_final: 0.7102 (mtp) REVERT: R 171 MET cc_start: 0.7951 (tpp) cc_final: 0.7646 (tpp) REVERT: R 243 LEU cc_start: 0.8627 (OUTLIER) cc_final: 0.8349 (mt) REVERT: A 28 GLU cc_start: 0.7346 (OUTLIER) cc_final: 0.7062 (tp30) REVERT: A 32 ARG cc_start: 0.7625 (ptp90) cc_final: 0.7120 (ptp90) REVERT: A 205 ARG cc_start: 0.7675 (pmt170) cc_final: 0.7386 (ppt90) REVERT: A 208 ARG cc_start: 0.5929 (mmm-85) cc_final: 0.5580 (tpt90) REVERT: A 276 GLU cc_start: 0.9025 (mp0) cc_final: 0.8690 (mp0) REVERT: A 294 ASN cc_start: 0.8756 (OUTLIER) cc_final: 0.8292 (t0) REVERT: A 298 GLU cc_start: 0.9220 (tp30) cc_final: 0.8784 (tt0) REVERT: B 78 LYS cc_start: 0.9095 (tppp) cc_final: 0.8819 (tptm) REVERT: B 217 MET cc_start: 0.6562 (OUTLIER) cc_final: 0.5622 (pp-130) REVERT: B 226 GLU cc_start: 0.8457 (mp0) cc_final: 0.8076 (mp0) REVERT: B 259 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.8071 (pt0) REVERT: B 294 CYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8044 (m) REVERT: B 336 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8888 (tp) REVERT: G 17 GLU cc_start: 0.9502 (tp30) cc_final: 0.9245 (tp30) REVERT: G 21 MET cc_start: 0.9055 (mmm) cc_final: 0.8769 (mmm) REVERT: G 41 CYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6424 (m) REVERT: S 13 GLN cc_start: 0.6108 (OUTLIER) cc_final: 0.5865 (pp30) REVERT: S 83 MET cc_start: 0.7558 (mtm) cc_final: 0.7131 (mtm) REVERT: S 93 MET cc_start: 0.8410 (ttt) cc_final: 0.8194 (ttt) REVERT: S 174 GLN cc_start: 0.8561 (tt0) cc_final: 0.8130 (mm-40) REVERT: S 207 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9132 (tm) outliers start: 38 outliers final: 11 residues processed: 152 average time/residue: 0.6128 time to fit residues: 98.7656 Evaluate side-chains 143 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 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 332 VAL Chi-restraints excluded: chain A residue 354 PHE Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS 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 41 CYS Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 100 optimal weight: 1.9990 chunk 76 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 1.9990 chunk 79 optimal weight: 5.9990 chunk 21 optimal weight: 0.1980 chunk 52 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 244 HIS ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** 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 = 0.3939 r_free = 0.3939 target = 0.106056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.082835 restraints weight = 21437.445| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.57 r_work: 0.3369 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.4304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8879 Z= 0.143 Angle : 0.736 13.804 12027 Z= 0.365 Chirality : 0.044 0.217 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.224 19.912 1217 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.25 % Allowed : 22.46 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.27), residues: 1085 helix: 1.46 (0.28), residues: 385 sheet: -0.29 (0.31), residues: 282 loop : -0.80 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 24 TYR 0.022 0.001 TYR B 59 PHE 0.021 0.001 PHE R 48 TRP 0.042 0.001 TRP R 184 HIS 0.010 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8876) covalent geometry : angle 0.73581 (12021) SS BOND : bond 0.00305 ( 3) SS BOND : angle 0.50700 ( 6) hydrogen bonds : bond 0.04416 ( 432) hydrogen bonds : angle 4.97439 ( 1212) *********************** 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 159 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 128 time to evaluate : 0.254 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 44 GLN cc_start: 0.8029 (mt0) cc_final: 0.7673 (mt0) REVERT: R 94 THR cc_start: 0.7464 (p) cc_final: 0.7233 (p) REVERT: R 151 MET cc_start: 0.7508 (mmm) cc_final: 0.7113 (mtp) REVERT: R 243 LEU cc_start: 0.8606 (OUTLIER) cc_final: 0.8312 (mt) REVERT: A 28 GLU cc_start: 0.7283 (OUTLIER) cc_final: 0.7021 (tp30) REVERT: A 32 ARG cc_start: 0.7710 (ptp90) cc_final: 0.7311 (ptp90) REVERT: A 205 ARG cc_start: 0.7711 (pmt170) cc_final: 0.7428 (ppt90) REVERT: A 208 ARG cc_start: 0.5920 (mmm-85) cc_final: 0.5503 (tpt90) REVERT: A 294 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8286 (t0) REVERT: A 298 GLU cc_start: 0.9161 (tp30) cc_final: 0.8758 (tt0) REVERT: B 78 LYS cc_start: 0.9043 (tppp) cc_final: 0.8708 (mptm) REVERT: B 176 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8622 (mt0) REVERT: B 211 TRP cc_start: 0.7132 (OUTLIER) cc_final: 0.4608 (m-10) REVERT: B 217 MET cc_start: 0.6442 (OUTLIER) cc_final: 0.5518 (pp-130) REVERT: B 226 GLU cc_start: 0.8476 (mp0) cc_final: 0.8107 (mp0) REVERT: B 259 GLN cc_start: 0.8416 (OUTLIER) cc_final: 0.8040 (pt0) REVERT: B 294 CYS cc_start: 0.8601 (OUTLIER) cc_final: 0.7987 (m) REVERT: G 15 LEU cc_start: 0.9266 (tm) cc_final: 0.9014 (mp) REVERT: G 41 CYS cc_start: 0.6917 (OUTLIER) cc_final: 0.6452 (m) REVERT: G 47 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8069 (pm20) REVERT: S 13 GLN cc_start: 0.6140 (OUTLIER) cc_final: 0.5885 (pp30) REVERT: S 83 MET cc_start: 0.7571 (mtm) cc_final: 0.7242 (mtm) REVERT: S 174 GLN cc_start: 0.8555 (tt0) cc_final: 0.8091 (mm-40) REVERT: S 206 ARG cc_start: 0.8763 (mpp-170) cc_final: 0.8218 (mpp-170) REVERT: S 207 LEU cc_start: 0.9383 (tm) cc_final: 0.8933 (tm) outliers start: 31 outliers final: 12 residues processed: 153 average time/residue: 0.6058 time to fit residues: 98.0439 Evaluate side-chains 143 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 121 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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 R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 294 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 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE 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 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 85 optimal weight: 0.3980 chunk 103 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 22 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** 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 = 0.3947 r_free = 0.3947 target = 0.106323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.083512 restraints weight = 21352.900| |-----------------------------------------------------------------------------| r_work (start): 0.3517 rms_B_bonded: 3.55 r_work: 0.3384 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.4414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 8879 Z= 0.145 Angle : 0.782 14.124 12027 Z= 0.381 Chirality : 0.044 0.223 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.235 19.720 1217 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.04 % Allowed : 24.03 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.27), residues: 1085 helix: 1.34 (0.28), residues: 387 sheet: -0.31 (0.30), residues: 282 loop : -0.85 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 27 TYR 0.013 0.001 TYR S 178 PHE 0.013 0.001 PHE B 253 TRP 0.046 0.001 TRP R 184 HIS 0.009 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00338 ( 8876) covalent geometry : angle 0.78195 (12021) SS BOND : bond 0.00272 ( 3) SS BOND : angle 0.53134 ( 6) hydrogen bonds : bond 0.04437 ( 432) hydrogen bonds : angle 5.03510 ( 1212) *********************** 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 160 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 131 time to evaluate : 0.382 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: 0.8043 (mt0) cc_final: 0.7763 (mt0) REVERT: R 94 THR cc_start: 0.7447 (p) cc_final: 0.7219 (p) REVERT: R 151 MET cc_start: 0.7505 (mmm) cc_final: 0.7066 (mtp) REVERT: R 171 MET cc_start: 0.7963 (tpp) cc_final: 0.7714 (tpp) REVERT: R 243 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8301 (mt) REVERT: R 290 GLU cc_start: 0.8949 (mm-30) cc_final: 0.8656 (mp0) REVERT: A 28 GLU cc_start: 0.7296 (OUTLIER) cc_final: 0.7033 (tp30) REVERT: A 32 ARG cc_start: 0.7824 (ptp90) cc_final: 0.7340 (ttm110) REVERT: A 205 ARG cc_start: 0.7679 (pmt170) cc_final: 0.7423 (ppt90) REVERT: A 208 ARG cc_start: 0.5852 (mmm-85) cc_final: 0.5412 (tpt90) REVERT: A 276 GLU cc_start: 0.9032 (mp0) cc_final: 0.8675 (mp0) REVERT: A 294 ASN cc_start: 0.8756 (m-40) cc_final: 0.8274 (t0) REVERT: A 298 GLU cc_start: 0.9163 (tp30) cc_final: 0.8763 (tt0) REVERT: B 78 LYS cc_start: 0.9029 (tppp) cc_final: 0.8699 (mptm) REVERT: B 176 GLN cc_start: 0.9167 (OUTLIER) cc_final: 0.8618 (mt0) REVERT: B 211 TRP cc_start: 0.7050 (OUTLIER) cc_final: 0.4591 (m-10) REVERT: B 217 MET cc_start: 0.6380 (OUTLIER) cc_final: 0.5420 (pp-130) REVERT: B 226 GLU cc_start: 0.8537 (mp0) cc_final: 0.8155 (mp0) REVERT: B 259 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.8072 (pt0) REVERT: B 294 CYS cc_start: 0.8603 (OUTLIER) cc_final: 0.7999 (m) REVERT: G 15 LEU cc_start: 0.9152 (tm) cc_final: 0.8752 (mt) REVERT: G 41 CYS cc_start: 0.6721 (OUTLIER) cc_final: 0.6334 (m) REVERT: G 47 GLU cc_start: 0.8978 (mm-30) cc_final: 0.8094 (pm20) REVERT: S 13 GLN cc_start: 0.6152 (OUTLIER) cc_final: 0.5904 (pp30) REVERT: S 83 MET cc_start: 0.7659 (mtm) cc_final: 0.7244 (mtm) REVERT: S 174 GLN cc_start: 0.8549 (tt0) cc_final: 0.8090 (mm-40) REVERT: S 207 LEU cc_start: 0.9275 (tm) cc_final: 0.9067 (tm) outliers start: 29 outliers final: 12 residues processed: 155 average time/residue: 0.5809 time to fit residues: 95.3478 Evaluate side-chains 143 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.258 ------------------------------------------------------------------------------- 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 R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 GLN 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 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 41 CYS 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 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 83 optimal weight: 6.9990 chunk 105 optimal weight: 4.9990 chunk 60 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 98 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 1.4984 ------------------------------------------------------------------------------- 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 ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** 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 = 0.3935 r_free = 0.3935 target = 0.105465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.082360 restraints weight = 21383.040| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 3.54 r_work: 0.3362 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.4498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 8879 Z= 0.171 Angle : 0.845 15.970 12027 Z= 0.408 Chirality : 0.046 0.307 1376 Planarity : 0.005 0.053 1499 Dihedral : 4.281 19.976 1217 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 2.94 % Allowed : 24.87 % Favored : 72.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.26), residues: 1085 helix: 1.29 (0.28), residues: 387 sheet: -0.42 (0.30), residues: 285 loop : -0.87 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG S 206 TYR 0.014 0.001 TYR S 178 PHE 0.012 0.001 PHE B 253 TRP 0.052 0.002 TRP R 184 HIS 0.009 0.002 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8876) covalent geometry : angle 0.84494 (12021) SS BOND : bond 0.00307 ( 3) SS BOND : angle 0.56431 ( 6) hydrogen bonds : bond 0.04681 ( 432) hydrogen bonds : angle 5.10819 ( 1212) ********************** 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 154 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.327 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: 0.8056 (mt0) cc_final: 0.7775 (mt0) REVERT: R 94 THR cc_start: 0.7521 (p) cc_final: 0.7316 (p) REVERT: R 151 MET cc_start: 0.7562 (mmm) cc_final: 0.7153 (mtt) REVERT: R 243 LEU cc_start: 0.8679 (OUTLIER) cc_final: 0.8407 (mt) REVERT: R 290 GLU cc_start: 0.8965 (mm-30) cc_final: 0.8671 (mp0) REVERT: A 28 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.7082 (tp30) REVERT: A 32 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7289 (ttm110) REVERT: A 205 ARG cc_start: 0.7781 (pmt170) cc_final: 0.7533 (ppt90) REVERT: A 276 GLU cc_start: 0.9069 (mp0) cc_final: 0.8772 (mp0) REVERT: A 294 ASN cc_start: 0.8764 (m-40) cc_final: 0.8292 (t0) REVERT: B 176 GLN cc_start: 0.9176 (OUTLIER) cc_final: 0.8639 (mt0) REVERT: B 211 TRP cc_start: 0.7149 (OUTLIER) cc_final: 0.4665 (m-10) REVERT: B 217 MET cc_start: 0.6399 (OUTLIER) cc_final: 0.5447 (pp-130) REVERT: B 226 GLU cc_start: 0.8544 (mp0) cc_final: 0.8164 (mp0) REVERT: B 259 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.8065 (pt0) REVERT: B 294 CYS cc_start: 0.8744 (OUTLIER) cc_final: 0.8146 (m) REVERT: G 15 LEU cc_start: 0.9210 (tm) cc_final: 0.8845 (mp) REVERT: G 20 LYS cc_start: 0.9463 (pptt) cc_final: 0.9256 (pmtt) REVERT: G 21 MET cc_start: 0.8640 (mmm) cc_final: 0.8325 (mmm) REVERT: G 41 CYS cc_start: 0.6864 (OUTLIER) cc_final: 0.6435 (m) REVERT: G 47 GLU cc_start: 0.8959 (mm-30) cc_final: 0.8085 (pm20) REVERT: S 13 GLN cc_start: 0.6170 (OUTLIER) cc_final: 0.5919 (pp30) REVERT: S 83 MET cc_start: 0.7687 (mtm) cc_final: 0.7229 (mtm) REVERT: S 174 GLN cc_start: 0.8566 (tt0) cc_final: 0.8096 (mm-40) REVERT: S 208 GLU cc_start: 0.8670 (pp20) cc_final: 0.8160 (pp20) outliers start: 28 outliers final: 12 residues processed: 148 average time/residue: 0.6049 time to fit residues: 94.7872 Evaluate side-chains 144 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 123 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 52 GLN Chi-restraints excluded: chain A residue 287 TYR 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 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 259 GLN Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 41 CYS 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 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 0.4980 chunk 21 optimal weight: 0.5980 chunk 54 optimal weight: 4.9990 chunk 77 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 103 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.106644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.083766 restraints weight = 21368.403| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 3.54 r_work: 0.3391 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7644 moved from start: 0.4612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8879 Z= 0.147 Angle : 0.827 14.496 12027 Z= 0.400 Chirality : 0.046 0.469 1376 Planarity : 0.005 0.050 1499 Dihedral : 4.258 20.340 1217 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 2.73 % Allowed : 25.29 % Favored : 71.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 1085 helix: 1.35 (0.28), residues: 387 sheet: -0.40 (0.30), residues: 284 loop : -0.86 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 24 TYR 0.012 0.001 TYR S 178 PHE 0.013 0.001 PHE B 253 TRP 0.052 0.001 TRP R 184 HIS 0.008 0.001 HIS B 225 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 8876) covalent geometry : angle 0.82763 (12021) SS BOND : bond 0.00313 ( 3) SS BOND : angle 0.43985 ( 6) hydrogen bonds : bond 0.04462 ( 432) hydrogen bonds : angle 5.01588 ( 1212) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3703.57 seconds wall clock time: 63 minutes 58.54 seconds (3838.54 seconds total)