Starting phenix.real_space_refine on Wed Jan 15 16:27:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yh0_39278/01_2025/8yh0_39278.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yh0_39278/01_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_39278/01_2025/8yh0_39278.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yh0_39278/01_2025/8yh0_39278.map" model { file = "/net/cci-nas-00/data/ceres_data/8yh0_39278/01_2025/8yh0_39278.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yh0_39278/01_2025/8yh0_39278.cif" } resolution = 2.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.004 sd= 1.047 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 66 5.16 5 C 5561 2.51 5 N 1463 2.21 5 O 1603 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 8693 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2198 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 8, 'TRANS': 262} Chain breaks: 1 Chain: "A" Number of atoms: 1700 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1700 Classifications: {'peptide': 211} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 208} Chain breaks: 2 Chain: "B" Number of atoms: 2583 Number of conformers: 1 Conformer: "" Number of residues, atoms: 336, 2583 Classifications: {'peptide': 336} Link IDs: {'PTRANS': 5, 'TRANS': 330} Chain: "G" Number of atoms: 407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 407 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 4, 'TRANS': 48} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'NEC': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.16, per 1000 atoms: 0.59 Number of scatterers: 8693 At special positions: 0 Unit cell: (90.37, 123.936, 123.936, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 66 16.00 O 1603 8.00 N 1463 7.00 C 5561 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 83 " - pdb=" SG CYS R 165 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.03 Simple disulfide: pdb=" SG CYS S 147 " - pdb=" SG CYS S 217 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 1.02 Creating SS restraints... Processing helix chain 'R' and resid 9 through 40 Processing helix chain 'R' and resid 41 through 44 Processing helix chain 'R' and resid 45 through 64 Processing helix chain 'R' and resid 64 through 75 Processing helix chain 'R' and resid 79 through 115 removed outlier: 3.534A pdb=" N CYS R 83 " --> pdb=" O HIS R 79 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR R 115 " --> pdb=" O ARG R 111 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 122 Processing helix chain 'R' and resid 123 through 144 Processing helix chain 'R' and resid 145 through 148 Processing helix chain 'R' and resid 150 through 154 Processing helix chain 'R' and resid 166 through 171 removed outlier: 3.533A pdb=" N VAL R 170 " --> pdb=" O ARG R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 172 through 179 Processing helix chain 'R' and resid 179 through 185 Processing helix chain 'R' and resid 185 through 207 Processing helix chain 'R' and resid 225 through 254 Proline residue: R 244 - end of helix Processing helix chain 'R' and resid 259 through 282 removed outlier: 3.688A pdb=" N MET R 275 " --> pdb=" O HIS R 271 " (cutoff:3.500A) Proline residue: R 278 - end of helix Processing helix chain 'R' and resid 285 through 295 Processing helix chain 'A' and resid 6 through 32 removed outlier: 3.880A pdb=" N ALA A 11 " --> pdb=" O ALA A 7 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 Processing helix chain 'A' and resid 211 through 216 removed outlier: 3.572A pdb=" N GLU A 216 " --> pdb=" O HIS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.817A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 349 Processing helix chain 'B' and resid 6 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.705A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N THR B 34 " --> pdb=" O LEU B 30 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 34' Processing helix chain 'G' and resid 10 through 24 removed outlier: 3.847A pdb=" N LEU G 15 " --> pdb=" O GLN G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'S' and resid 28 through 32 Processing helix chain 'S' and resid 87 through 91 removed outlier: 4.025A pdb=" N THR S 91 " --> pdb=" O SER S 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 212 removed outlier: 3.955A pdb=" N VAL S 212 " --> pdb=" O ALA S 209 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 6.910A pdb=" N LYS A 35 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 222 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU A 37 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N CYS A 224 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N LEU A 39 " --> pdb=" O CYS A 224 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ILE A 221 " --> pdb=" O ILE A 265 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N PHE A 267 " --> pdb=" O ILE A 221 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N PHE A 223 " --> pdb=" O PHE A 267 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE A 264 " --> pdb=" O TYR A 320 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N HIS A 322 " --> pdb=" O ILE A 264 " (cutoff:3.500A) removed outlier: 7.060A pdb=" N LEU A 266 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.635A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.138A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.496A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.899A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.815A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N ILE B 157 " --> pdb=" O TRP B 169 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 7.028A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.392A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.409A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.977A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.472A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N CYS B 294 " --> pdb=" O VAL B 307 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VAL B 307 " --> pdb=" O CYS B 294 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL B 296 " --> pdb=" O ALA B 305 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 6.278A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLY S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 128 through 130 removed outlier: 3.555A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 134 through 136 removed outlier: 6.189A pdb=" N VAL S 135 " --> pdb=" O GLU S 234 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N TRP S 164 " --> pdb=" O LEU S 176 " (cutoff:3.500A) 432 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.62 Time building geometry restraints manager: 2.87 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: 0.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.300 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 22.530 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.700 ------------------------------------------------------------------------------- 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 8876 Z= 0.289 Angle : 0.656 14.994 12021 Z= 0.361 Chirality : 0.063 1.697 1376 Planarity : 0.004 0.050 1499 Dihedral : 13.132 77.755 3199 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.69 % Favored : 96.22 % Rotamer: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1085 helix: 1.45 (0.28), residues: 363 sheet: -0.82 (0.29), residues: 293 loop : -0.57 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 82 HIS 0.003 0.001 HIS B 62 PHE 0.018 0.001 PHE B 234 TYR 0.012 0.001 TYR S 178 ARG 0.003 0.000 ARG B 314 *********************** 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 : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LEU cc_start: 0.8608 (mt) cc_final: 0.8191 (mt) outliers start: 0 outliers final: 1 residues processed: 226 average time/residue: 1.3943 time to fit residues: 333.1278 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 129 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 36 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 3.9990 chunk 82 optimal weight: 8.9990 chunk 45 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 55 optimal weight: 0.0770 chunk 44 optimal weight: 5.9990 chunk 85 optimal weight: 20.0000 chunk 33 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 overall best weight: 2.4146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 30 ASN R 79 HIS ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS A 255 ASN A 294 ASN ** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 176 GLN B 295 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.106171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.082742 restraints weight = 20868.367| |-----------------------------------------------------------------------------| r_work (start): 0.3486 rms_B_bonded: 3.44 r_work: 0.3352 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 8876 Z= 0.323 Angle : 0.734 11.181 12021 Z= 0.375 Chirality : 0.046 0.233 1376 Planarity : 0.005 0.069 1499 Dihedral : 5.088 51.720 1219 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.15 % Allowed : 12.80 % Favored : 84.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.26), residues: 1085 helix: 1.38 (0.27), residues: 370 sheet: -0.66 (0.29), residues: 297 loop : -0.63 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP R 184 HIS 0.007 0.001 HIS A 322 PHE 0.017 0.002 PHE B 199 TYR 0.017 0.002 TYR A 302 ARG 0.007 0.001 ARG S 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 147 time to evaluate : 0.962 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: 0.7603 (p) cc_final: 0.7342 (p) REVERT: A 298 GLU cc_start: 0.9207 (tp30) cc_final: 0.8798 (tt0) REVERT: B 176 GLN cc_start: 0.9072 (OUTLIER) cc_final: 0.8590 (mt0) REVERT: B 226 GLU cc_start: 0.7872 (mp0) cc_final: 0.7635 (mp0) REVERT: B 259 GLN cc_start: 0.8134 (tt0) cc_final: 0.7915 (pt0) REVERT: B 336 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8613 (mp) REVERT: S 174 GLN cc_start: 0.8558 (tt0) cc_final: 0.8204 (mm-40) REVERT: S 206 ARG cc_start: 0.8700 (mmm-85) cc_final: 0.8426 (mmm-85) REVERT: S 207 LEU cc_start: 0.9348 (OUTLIER) cc_final: 0.9132 (tm) outliers start: 30 outliers final: 12 residues processed: 166 average time/residue: 1.3889 time to fit residues: 244.2826 Evaluate side-chains 130 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 59 ILE Chi-restraints excluded: chain R residue 138 SER Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain G residue 57 SER Chi-restraints excluded: chain S residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 51 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 89 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 chunk 86 optimal weight: 8.9990 chunk 40 optimal weight: 30.0000 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 213 HIS A 322 HIS B 176 GLN B 266 HIS ** S 130 GLN ** 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 = 0.3950 r_free = 0.3950 target = 0.106713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.083503 restraints weight = 21057.467| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.47 r_work: 0.3378 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.3339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8876 Z= 0.228 Angle : 0.671 12.591 12021 Z= 0.344 Chirality : 0.044 0.246 1376 Planarity : 0.004 0.050 1499 Dihedral : 4.780 50.816 1219 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 3.57 % Allowed : 16.47 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.27), residues: 1085 helix: 1.67 (0.28), residues: 364 sheet: -0.41 (0.29), residues: 288 loop : -0.63 (0.32), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP R 184 HIS 0.005 0.001 HIS A 322 PHE 0.014 0.001 PHE B 253 TYR 0.012 0.001 TYR S 178 ARG 0.008 0.001 ARG G 13 *********************** 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 163 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 129 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 94 THR cc_start: 0.7467 (p) cc_final: 0.7218 (p) REVERT: R 243 LEU cc_start: 0.8762 (OUTLIER) cc_final: 0.8522 (mt) REVERT: A 28 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7241 (tp30) REVERT: A 32 ARG cc_start: 0.7686 (ptp90) cc_final: 0.7246 (ptp90) REVERT: A 208 ARG cc_start: 0.5927 (mmm-85) cc_final: 0.5623 (tpt90) REVERT: A 287 TYR cc_start: 0.6457 (t80) cc_final: 0.6242 (t80) REVERT: A 298 GLU cc_start: 0.9220 (tp30) cc_final: 0.8800 (tt0) REVERT: B 78 LYS cc_start: 0.9169 (tppp) cc_final: 0.8813 (tptm) REVERT: B 188 MET cc_start: 0.8773 (mmm) cc_final: 0.8560 (mmm) REVERT: B 217 MET cc_start: 0.6416 (OUTLIER) cc_final: 0.5507 (pp-130) REVERT: B 226 GLU cc_start: 0.8018 (mp0) cc_final: 0.7695 (mp0) REVERT: S 93 MET cc_start: 0.8359 (ttt) cc_final: 0.8032 (tmt) REVERT: S 174 GLN cc_start: 0.8554 (tt0) cc_final: 0.8205 (mm-40) REVERT: S 206 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8509 (mmm-85) outliers start: 34 outliers final: 12 residues processed: 154 average time/residue: 1.3270 time to fit residues: 216.6656 Evaluate side-chains 135 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 120 time to evaluate : 1.057 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain R residue 265 LEU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 129 THR 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 85 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 3 optimal weight: 7.9990 chunk 44 optimal weight: 10.0000 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 67 optimal weight: 0.7980 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 271 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 277 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN ** A 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 259 GLN S 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.103476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.080468 restraints weight = 21228.943| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 3.42 r_work: 0.3322 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.3732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 8876 Z= 0.337 Angle : 0.701 12.125 12021 Z= 0.358 Chirality : 0.045 0.261 1376 Planarity : 0.005 0.054 1499 Dihedral : 4.863 49.354 1219 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.87 % Favored : 96.04 % Rotamer: Outliers : 4.20 % Allowed : 17.63 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.26), residues: 1085 helix: 1.54 (0.28), residues: 365 sheet: -0.54 (0.30), residues: 291 loop : -0.65 (0.32), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP R 184 HIS 0.006 0.002 HIS B 225 PHE 0.015 0.002 PHE B 199 TYR 0.023 0.002 TYR A 302 ARG 0.006 0.001 ARG A 24 *********************** 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 167 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 127 time to evaluate : 0.992 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: 0.8480 (mt0) cc_final: 0.7945 (mp10) REVERT: R 290 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8663 (mp0) REVERT: A 28 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7281 (tp30) REVERT: A 32 ARG cc_start: 0.7776 (ptp90) cc_final: 0.7424 (ttm110) REVERT: A 294 ASN cc_start: 0.8919 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 298 GLU cc_start: 0.9213 (tp30) cc_final: 0.8763 (tt0) REVERT: A 353 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7779 (tt) REVERT: B 14 LEU cc_start: 0.9209 (mt) cc_final: 0.8991 (mt) REVERT: B 44 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.8395 (mt0) REVERT: B 78 LYS cc_start: 0.9114 (tppp) cc_final: 0.8791 (tptm) REVERT: B 176 GLN cc_start: 0.9156 (OUTLIER) cc_final: 0.8679 (mt0) REVERT: B 211 TRP cc_start: 0.7434 (OUTLIER) cc_final: 0.4755 (m-10) REVERT: B 217 MET cc_start: 0.6395 (OUTLIER) cc_final: 0.5493 (pp-130) REVERT: B 226 GLU cc_start: 0.8057 (mp0) cc_final: 0.7695 (mp0) REVERT: G 47 GLU cc_start: 0.7422 (pm20) cc_final: 0.7207 (pm20) REVERT: S 13 GLN cc_start: 0.5953 (OUTLIER) cc_final: 0.5652 (pp30) REVERT: S 83 MET cc_start: 0.7491 (OUTLIER) cc_final: 0.7149 (mtm) REVERT: S 93 MET cc_start: 0.8341 (ttt) cc_final: 0.8000 (tmt) REVERT: S 174 GLN cc_start: 0.8581 (tt0) cc_final: 0.8192 (mm-40) REVERT: S 206 ARG cc_start: 0.8815 (mmm-85) cc_final: 0.8510 (mmm-85) outliers start: 40 outliers final: 18 residues processed: 159 average time/residue: 1.3126 time to fit residues: 221.7212 Evaluate side-chains 145 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 118 time to evaluate : 1.138 ------------------------------------------------------------------------------- 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 191 VAL Chi-restraints excluded: chain R residue 195 ILE Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 44 GLN Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 233 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 5 optimal weight: 0.9980 chunk 73 optimal weight: 6.9990 chunk 50 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 88 optimal weight: 7.9990 chunk 41 optimal weight: 0.0070 chunk 51 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- 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 244 HIS ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3900 r_free = 0.3900 target = 0.103480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.080392 restraints weight = 21005.383| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 3.42 r_work: 0.3320 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 8876 Z= 0.304 Angle : 0.699 13.396 12021 Z= 0.355 Chirality : 0.045 0.202 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.624 21.209 1217 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 4.41 % Allowed : 18.68 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.26), residues: 1085 helix: 1.32 (0.28), residues: 378 sheet: -0.39 (0.30), residues: 284 loop : -0.75 (0.32), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP R 184 HIS 0.012 0.002 HIS B 225 PHE 0.016 0.002 PHE B 199 TYR 0.029 0.002 TYR A 302 ARG 0.006 0.001 ARG A 24 *********************** 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 170 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 128 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 LEU cc_start: 0.8860 (mp) cc_final: 0.8623 (mp) REVERT: R 44 GLN cc_start: 0.8495 (mt0) cc_final: 0.7961 (mp10) REVERT: R 90 MET cc_start: 0.7482 (mtp) cc_final: 0.7281 (mtm) REVERT: R 146 MET cc_start: 0.7518 (OUTLIER) cc_final: 0.7228 (mmm) REVERT: R 151 MET cc_start: 0.7601 (mmm) cc_final: 0.7234 (mtt) REVERT: R 171 MET cc_start: 0.7960 (tpp) cc_final: 0.7581 (tpp) REVERT: R 243 LEU cc_start: 0.8761 (OUTLIER) cc_final: 0.8499 (mt) REVERT: A 28 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7196 (tp30) REVERT: A 32 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7513 (ptp90) REVERT: A 205 ARG cc_start: 0.7702 (pmt170) cc_final: 0.7392 (ppt90) REVERT: A 294 ASN cc_start: 0.8897 (OUTLIER) cc_final: 0.8504 (t0) REVERT: A 298 GLU cc_start: 0.9272 (tp30) cc_final: 0.8756 (tt0) REVERT: B 78 LYS cc_start: 0.9149 (tppp) cc_final: 0.8855 (tptm) REVERT: B 176 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8697 (mt0) REVERT: B 211 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.5187 (m-90) REVERT: B 217 MET cc_start: 0.6527 (OUTLIER) cc_final: 0.5599 (pp-130) REVERT: B 226 GLU cc_start: 0.8240 (mp0) cc_final: 0.7769 (mp0) REVERT: B 262 MET cc_start: 0.8244 (tpp) cc_final: 0.7811 (mmm) REVERT: G 21 MET cc_start: 0.8978 (mmm) cc_final: 0.8512 (mpm) REVERT: S 13 GLN cc_start: 0.6185 (OUTLIER) cc_final: 0.5939 (pp30) REVERT: S 83 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.7111 (mtm) REVERT: S 174 GLN cc_start: 0.8592 (tt0) cc_final: 0.8180 (mm-40) outliers start: 42 outliers final: 18 residues processed: 160 average time/residue: 1.2501 time to fit residues: 212.5906 Evaluate side-chains 146 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 119 time to evaluate : 1.014 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain R residue 146 MET Chi-restraints excluded: chain R residue 234 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 172 GLU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 211 TRP Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 83 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 53 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 106 optimal weight: 6.9990 chunk 36 optimal weight: 4.9990 chunk 4 optimal weight: 0.9980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 3.9990 chunk 57 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- 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 244 HIS ** A 269 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.104159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.081289 restraints weight = 20716.322| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 3.41 r_work: 0.3342 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3342 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 8876 Z= 0.242 Angle : 0.698 13.109 12021 Z= 0.349 Chirality : 0.044 0.189 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.502 21.259 1217 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.78 % Favored : 96.13 % Rotamer: Outliers : 4.20 % Allowed : 20.15 % Favored : 75.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.26), residues: 1085 helix: 1.34 (0.28), residues: 378 sheet: -0.41 (0.31), residues: 276 loop : -0.72 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP R 184 HIS 0.011 0.001 HIS B 225 PHE 0.014 0.001 PHE B 253 TYR 0.024 0.001 TYR A 302 ARG 0.007 0.001 ARG A 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2170 Ramachandran restraints generated. 1085 Oldfield, 0 Emsley, 1085 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 125 time to evaluate : 0.959 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: 0.8416 (mt0) cc_final: 0.7932 (mp10) REVERT: R 243 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8467 (mt) REVERT: R 276 MET cc_start: 0.8453 (tmm) cc_final: 0.8248 (tmm) REVERT: A 28 GLU cc_start: 0.7453 (OUTLIER) cc_final: 0.7196 (tm-30) REVERT: A 32 ARG cc_start: 0.7720 (ptp90) cc_final: 0.7459 (mtm110) REVERT: A 205 ARG cc_start: 0.7714 (pmt170) cc_final: 0.7407 (ppt90) REVERT: A 294 ASN cc_start: 0.8879 (OUTLIER) cc_final: 0.8439 (t0) REVERT: A 298 GLU cc_start: 0.9217 (tp30) cc_final: 0.8694 (tt0) REVERT: A 353 LEU cc_start: 0.8155 (OUTLIER) cc_final: 0.7914 (tt) REVERT: B 44 GLN cc_start: 0.8839 (OUTLIER) cc_final: 0.8340 (mt0) REVERT: B 78 LYS cc_start: 0.9125 (tppp) cc_final: 0.8842 (tptm) REVERT: B 176 GLN cc_start: 0.9164 (OUTLIER) cc_final: 0.8641 (mt0) REVERT: B 211 TRP cc_start: 0.7398 (OUTLIER) cc_final: 0.5115 (m-90) REVERT: B 217 MET cc_start: 0.6619 (OUTLIER) cc_final: 0.5691 (pp-130) REVERT: B 226 GLU cc_start: 0.8319 (mp0) cc_final: 0.7930 (mp0) REVERT: B 262 MET cc_start: 0.8253 (tpp) cc_final: 0.7751 (mmm) REVERT: G 17 GLU cc_start: 0.9577 (tp30) cc_final: 0.9369 (tp30) REVERT: S 13 GLN cc_start: 0.6158 (OUTLIER) cc_final: 0.5912 (pp30) REVERT: S 174 GLN cc_start: 0.8552 (tt0) cc_final: 0.8159 (mm-40) outliers start: 40 outliers final: 16 residues processed: 154 average time/residue: 1.3615 time to fit residues: 222.3258 Evaluate side-chains 146 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 121 time to evaluate : 1.034 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 331 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 LEU 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 316 SER Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 145 ILE Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 52 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 1.9990 chunk 81 optimal weight: 0.0040 chunk 64 optimal weight: 7.9990 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 3.9990 chunk 40 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 overall best weight: 2.4000 ------------------------------------------------------------------------------- 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 244 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 225 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.103213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.079611 restraints weight = 21499.866| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 3.58 r_work: 0.3306 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7664 moved from start: 0.4259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 8876 Z= 0.307 Angle : 0.748 13.634 12021 Z= 0.372 Chirality : 0.045 0.208 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.595 21.175 1217 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.59 % Favored : 96.31 % Rotamer: Outliers : 4.30 % Allowed : 21.72 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.26), residues: 1085 helix: 1.47 (0.28), residues: 370 sheet: -0.54 (0.30), residues: 283 loop : -0.68 (0.32), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP R 184 HIS 0.011 0.002 HIS B 225 PHE 0.030 0.002 PHE R 48 TYR 0.020 0.002 TYR A 302 ARG 0.007 0.001 ARG G 27 *********************** 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 167 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 126 time to evaluate : 0.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 40 ASN cc_start: 0.8364 (t0) cc_final: 0.7709 (t0) REVERT: R 44 GLN cc_start: 0.8331 (mt0) cc_final: 0.7853 (mp10) REVERT: R 151 MET cc_start: 0.7671 (mmm) cc_final: 0.7157 (mtp) REVERT: R 171 MET cc_start: 0.8099 (tpp) cc_final: 0.7785 (tpp) REVERT: R 243 LEU cc_start: 0.8645 (OUTLIER) cc_final: 0.8361 (mt) REVERT: R 290 GLU cc_start: 0.9051 (mm-30) cc_final: 0.8728 (mp0) REVERT: A 28 GLU cc_start: 0.7370 (OUTLIER) cc_final: 0.7079 (tm-30) REVERT: A 32 ARG cc_start: 0.7685 (ptp90) cc_final: 0.7386 (mtm110) REVERT: A 205 ARG cc_start: 0.7802 (pmt170) cc_final: 0.7485 (ppt90) REVERT: A 294 ASN cc_start: 0.8920 (m-40) cc_final: 0.8580 (t0) REVERT: A 353 LEU cc_start: 0.8136 (OUTLIER) cc_final: 0.7852 (tt) REVERT: B 78 LYS cc_start: 0.8965 (tppp) cc_final: 0.8693 (tptm) REVERT: B 176 GLN cc_start: 0.9177 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: B 211 TRP cc_start: 0.7398 (OUTLIER) cc_final: 0.5079 (m-90) REVERT: B 217 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.5684 (pp-130) REVERT: B 226 GLU cc_start: 0.8502 (mp0) cc_final: 0.8110 (mp0) REVERT: B 336 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8848 (tp) REVERT: S 13 GLN cc_start: 0.6148 (OUTLIER) cc_final: 0.5904 (pp30) REVERT: S 162 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7535 (tp) REVERT: S 174 GLN cc_start: 0.8572 (tt0) cc_final: 0.8013 (mm-40) outliers start: 41 outliers final: 19 residues processed: 159 average time/residue: 1.3163 time to fit residues: 222.1815 Evaluate side-chains 149 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 0.986 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 343 ILE Chi-restraints excluded: chain A residue 353 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 307 VAL 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 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain G residue 36 ASP Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 128 MET Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 233 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 72 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- 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 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 244 HIS ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.104267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.081366 restraints weight = 21197.358| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 3.46 r_work: 0.3343 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8876 Z= 0.232 Angle : 0.752 13.784 12021 Z= 0.374 Chirality : 0.045 0.216 1376 Planarity : 0.004 0.052 1499 Dihedral : 4.471 20.851 1217 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.41 % Favored : 96.50 % Rotamer: Outliers : 3.88 % Allowed : 23.50 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.26), residues: 1085 helix: 1.34 (0.28), residues: 381 sheet: -0.46 (0.31), residues: 282 loop : -0.86 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.001 TRP R 184 HIS 0.009 0.001 HIS B 225 PHE 0.014 0.001 PHE B 253 TYR 0.014 0.001 TYR S 178 ARG 0.010 0.001 ARG S 18 *********************** 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 164 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 127 time to evaluate : 0.944 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 LEU cc_start: 0.8723 (mp) cc_final: 0.8445 (mp) REVERT: R 44 GLN cc_start: 0.8272 (mt0) cc_final: 0.7883 (mp10) REVERT: R 151 MET cc_start: 0.7605 (mmm) cc_final: 0.7053 (mtp) REVERT: R 171 MET cc_start: 0.7988 (tpp) cc_final: 0.7704 (tpp) REVERT: R 243 LEU cc_start: 0.8680 (OUTLIER) cc_final: 0.8414 (mt) REVERT: R 290 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8668 (mp0) REVERT: A 28 GLU cc_start: 0.7407 (OUTLIER) cc_final: 0.7198 (tm-30) REVERT: A 32 ARG cc_start: 0.7692 (ptp90) cc_final: 0.7437 (mtm110) REVERT: A 208 ARG cc_start: 0.6190 (mmm-85) cc_final: 0.5773 (tpt90) REVERT: A 294 ASN cc_start: 0.8890 (OUTLIER) cc_final: 0.8411 (t0) REVERT: A 353 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7927 (tt) REVERT: B 78 LYS cc_start: 0.9092 (tppp) cc_final: 0.8824 (tptm) REVERT: B 176 GLN cc_start: 0.9151 (OUTLIER) cc_final: 0.8628 (mt0) REVERT: B 211 TRP cc_start: 0.7360 (OUTLIER) cc_final: 0.4957 (m-90) REVERT: B 217 MET cc_start: 0.6551 (OUTLIER) cc_final: 0.5598 (pp-130) REVERT: B 226 GLU cc_start: 0.8476 (mp0) cc_final: 0.8051 (mp0) REVERT: B 294 CYS cc_start: 0.8685 (OUTLIER) cc_final: 0.8174 (m) REVERT: B 336 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8923 (tp) REVERT: G 15 LEU cc_start: 0.9395 (tm) cc_final: 0.9029 (mt) REVERT: S 13 GLN cc_start: 0.6256 (OUTLIER) cc_final: 0.6003 (pp30) REVERT: S 73 ASP cc_start: 0.7006 (t0) cc_final: 0.6711 (t70) REVERT: S 76 LYS cc_start: 0.8631 (ptmm) cc_final: 0.8364 (ptmm) REVERT: S 87 ARG cc_start: 0.8030 (ptp-170) cc_final: 0.7686 (pmm-80) REVERT: S 162 LEU cc_start: 0.7991 (OUTLIER) cc_final: 0.7775 (tp) REVERT: S 174 GLN cc_start: 0.8583 (tt0) cc_final: 0.8131 (mm-40) outliers start: 37 outliers final: 12 residues processed: 156 average time/residue: 1.3024 time to fit residues: 216.1087 Evaluate side-chains 145 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 122 time to evaluate : 1.042 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 294 ASN Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain A residue 353 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 294 CYS Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 87 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 96 optimal weight: 0.0170 chunk 32 optimal weight: 4.9990 chunk 56 optimal weight: 0.9980 overall best weight: 1.1420 ------------------------------------------------------------------------------- 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 255 ASN ** A 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.105188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.082255 restraints weight = 21117.654| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.48 r_work: 0.3363 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.4490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8876 Z= 0.223 Angle : 0.782 14.222 12021 Z= 0.386 Chirality : 0.045 0.234 1376 Planarity : 0.005 0.052 1499 Dihedral : 4.435 20.449 1217 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.73 % Allowed : 24.45 % Favored : 72.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.26), residues: 1085 helix: 1.42 (0.28), residues: 381 sheet: -0.41 (0.31), residues: 282 loop : -0.93 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP R 184 HIS 0.008 0.001 HIS B 225 PHE 0.014 0.001 PHE B 253 TYR 0.014 0.001 TYR S 178 ARG 0.011 0.001 ARG A 24 *********************** 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 157 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 131 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 43 LEU cc_start: 0.8646 (mp) cc_final: 0.8403 (mp) REVERT: R 44 GLN cc_start: 0.8307 (mt0) cc_final: 0.7900 (mp10) REVERT: R 151 MET cc_start: 0.7561 (mmm) cc_final: 0.6990 (mtp) REVERT: R 171 MET cc_start: 0.8034 (tpp) cc_final: 0.7723 (tpp) REVERT: R 173 MET cc_start: 0.8529 (mmm) cc_final: 0.8206 (mmp) REVERT: R 192 MET cc_start: 0.7453 (mtm) cc_final: 0.7246 (mtp) REVERT: R 243 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8489 (mt) REVERT: R 286 LYS cc_start: 0.9174 (mppt) cc_final: 0.8685 (mppt) REVERT: R 290 GLU cc_start: 0.8891 (mm-30) cc_final: 0.8642 (mp0) REVERT: A 32 ARG cc_start: 0.7788 (ptp90) cc_final: 0.7541 (mtm110) REVERT: A 208 ARG cc_start: 0.6085 (mmm-85) cc_final: 0.5721 (tpt90) REVERT: A 294 ASN cc_start: 0.8786 (m-40) cc_final: 0.8241 (t0) REVERT: B 176 GLN cc_start: 0.9137 (OUTLIER) cc_final: 0.8620 (mt0) REVERT: B 217 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.5607 (pp-130) REVERT: B 226 GLU cc_start: 0.8535 (mp0) cc_final: 0.8143 (mp0) REVERT: B 294 CYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8088 (m) REVERT: G 15 LEU cc_start: 0.9383 (tm) cc_final: 0.9071 (mt) REVERT: G 20 LYS cc_start: 0.9552 (pptt) cc_final: 0.9307 (pptt) REVERT: S 13 GLN cc_start: 0.6288 (OUTLIER) cc_final: 0.6037 (pp30) REVERT: S 73 ASP cc_start: 0.7092 (t0) cc_final: 0.6743 (t70) REVERT: S 162 LEU cc_start: 0.8028 (OUTLIER) cc_final: 0.7819 (tp) REVERT: S 174 GLN cc_start: 0.8579 (tt0) cc_final: 0.8179 (mm-40) REVERT: S 206 ARG cc_start: 0.8772 (mpp-170) cc_final: 0.8314 (mpp-170) outliers start: 26 outliers final: 14 residues processed: 151 average time/residue: 1.3582 time to fit residues: 217.4019 Evaluate side-chains 140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 243 LEU Chi-restraints excluded: chain R residue 247 ILE Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 332 VAL Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER 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 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 7 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 69 optimal weight: 10.0000 chunk 91 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 34 optimal weight: 8.9990 chunk 76 optimal weight: 0.2980 chunk 51 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.103431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.080517 restraints weight = 21211.314| |-----------------------------------------------------------------------------| r_work (start): 0.3471 rms_B_bonded: 3.46 r_work: 0.3332 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7771 moved from start: 0.4624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 8876 Z= 0.303 Angle : 0.838 14.548 12021 Z= 0.416 Chirality : 0.046 0.259 1376 Planarity : 0.005 0.052 1499 Dihedral : 4.610 21.588 1217 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 3.04 % Allowed : 25.08 % Favored : 71.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.45 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.26), residues: 1085 helix: 1.24 (0.27), residues: 381 sheet: -0.53 (0.30), residues: 283 loop : -0.95 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.002 TRP R 184 HIS 0.010 0.001 HIS B 225 PHE 0.014 0.002 PHE B 253 TYR 0.015 0.001 TYR S 178 ARG 0.011 0.001 ARG A 24 ********************** 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 153 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.005 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: R 43 LEU cc_start: 0.8738 (mp) cc_final: 0.8495 (mp) REVERT: R 44 GLN cc_start: 0.8381 (mt0) cc_final: 0.7930 (mp10) REVERT: R 151 MET cc_start: 0.7720 (mmm) cc_final: 0.7361 (mtp) REVERT: R 171 MET cc_start: 0.8067 (tpp) cc_final: 0.7765 (tpp) REVERT: R 173 MET cc_start: 0.8469 (mmm) cc_final: 0.8181 (mmp) REVERT: R 243 LEU cc_start: 0.8752 (OUTLIER) cc_final: 0.8474 (mt) REVERT: A 205 ARG cc_start: 0.7819 (pmt170) cc_final: 0.7267 (pmt-80) REVERT: A 294 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8310 (t0) REVERT: B 176 GLN cc_start: 0.9171 (OUTLIER) cc_final: 0.8661 (mt0) REVERT: B 217 MET cc_start: 0.6554 (OUTLIER) cc_final: 0.5618 (pp-130) REVERT: B 226 GLU cc_start: 0.8576 (mp0) cc_final: 0.8167 (mp0) REVERT: B 294 CYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8130 (m) REVERT: S 13 GLN cc_start: 0.6319 (OUTLIER) cc_final: 0.6075 (pp30) REVERT: S 73 ASP cc_start: 0.7007 (t0) cc_final: 0.6643 (t70) REVERT: S 109 ASP cc_start: 0.8144 (p0) cc_final: 0.7937 (p0) REVERT: S 162 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7716 (tp) REVERT: S 174 GLN cc_start: 0.8586 (tt0) cc_final: 0.8132 (mm-40) outliers start: 29 outliers final: 15 residues processed: 146 average time/residue: 1.3109 time to fit residues: 203.4146 Evaluate side-chains 141 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 119 time to evaluate : 1.140 ------------------------------------------------------------------------------- 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 141 VAL Chi-restraints excluded: chain R residue 243 LEU Chi-restraints excluded: chain R residue 251 ILE Chi-restraints excluded: chain A residue 243 MET Chi-restraints excluded: chain A residue 287 TYR 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 217 MET Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 307 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 31 SER Chi-restraints excluded: chain S residue 13 GLN Chi-restraints excluded: chain S residue 129 THR Chi-restraints excluded: chain S residue 162 LEU Chi-restraints excluded: chain S residue 235 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 54 optimal weight: 0.8980 chunk 12 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 42 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 90 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 81 optimal weight: 9.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 269 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.104884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.081959 restraints weight = 21134.895| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.48 r_work: 0.3356 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8876 Z= 0.255 Angle : 0.846 14.496 12021 Z= 0.415 Chirality : 0.046 0.221 1376 Planarity : 0.005 0.067 1499 Dihedral : 4.532 27.184 1217 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 12.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.31 % Allowed : 25.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.26), residues: 1085 helix: 1.30 (0.28), residues: 382 sheet: -0.51 (0.30), residues: 283 loop : -0.94 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP R 184 HIS 0.009 0.001 HIS B 225 PHE 0.032 0.001 PHE R 48 TYR 0.013 0.001 TYR S 178 ARG 0.013 0.001 ARG S 206 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7467.50 seconds wall clock time: 132 minutes 33.07 seconds (7953.07 seconds total)