Starting phenix.real_space_refine on Fri Jul 25 05:33:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.map" model { file = "/net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ld3_23280/07_2025/7ld3_23280.cif" } resolution = 3.2 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= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 53 5.16 5 Cl 1 4.86 5 C 4498 2.51 5 N 1189 2.21 5 O 1269 1.98 5 F 6 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 7016 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1693 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 207} Chain breaks: 2 Chain: "R" Number of atoms: 2273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 288, 2273 Classifications: {'peptide': 288} Link IDs: {'PTRANS': 14, 'TRANS': 273} Chain breaks: 1 Chain: "B" Number of atoms: 2568 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2568 Classifications: {'peptide': 334} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 328} Chain breaks: 1 Chain: "G" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 433 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 49 Unusual residues: {'ADN%rna3p': 1, 'XTD': 1} Classifications: {'undetermined': 2, 'water': 1} Modifications used: {'rna3p': 1} Link IDs: {None: 2} Time building chain proxies: 4.70, per 1000 atoms: 0.67 Number of scatterers: 7016 At special positions: 0 Unit cell: (127.204, 88.382, 102.424, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 53 16.00 F 6 9.00 O 1269 8.00 N 1189 7.00 C 4498 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS R 80 " - pdb=" SG CYS R 169 " distance=2.03 Simple disulfide: pdb=" SG CYS R 260 " - pdb=" SG CYS R 263 " 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: 1.61 Conformation dependent library (CDL) restraints added in 972.2 milliseconds 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1684 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 9 sheets defined 47.1% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 11 through 30 removed outlier: 3.702A pdb=" N ARG A 15 " --> pdb=" O ALA A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.671A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 217 removed outlier: 4.834A pdb=" N ILE A 213 " --> pdb=" O LYS A 210 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N HIS A 214 " --> pdb=" O LYS A 211 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N PHE A 216 " --> pdb=" O ILE A 213 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU A 217 " --> pdb=" O HIS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 4.105A pdb=" N ASP A 232 " --> pdb=" O SER A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 242 through 256 removed outlier: 3.526A pdb=" N ASN A 256 " --> pdb=" O ASP A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 282 removed outlier: 3.644A pdb=" N GLU A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR A 280 " --> pdb=" O GLU A 276 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N HIS A 281 " --> pdb=" O GLU A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 296 through 310 Processing helix chain 'A' and resid 328 through 353 removed outlier: 3.704A pdb=" N ASN A 332 " --> pdb=" O THR A 328 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N VAL A 333 " --> pdb=" O ASP A 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 6 through 36 removed outlier: 3.715A pdb=" N ALA R 10 " --> pdb=" O SER R 6 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA R 11 " --> pdb=" O ALA R 7 " (cutoff:3.500A) Proline residue: R 25 - end of helix Processing helix chain 'R' and resid 42 through 62 Processing helix chain 'R' and resid 62 through 72 Processing helix chain 'R' and resid 77 through 111 Proline residue: R 86 - end of helix Processing helix chain 'R' and resid 120 through 140 Processing helix chain 'R' and resid 141 through 144 Processing helix chain 'R' and resid 148 through 160 Processing helix chain 'R' and resid 170 through 175 removed outlier: 3.664A pdb=" N VAL R 174 " --> pdb=" O GLU R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 176 through 183 Processing helix chain 'R' and resid 184 through 189 Processing helix chain 'R' and resid 189 through 211 Processing helix chain 'R' and resid 225 through 260 Proline residue: R 249 - end of helix Processing helix chain 'R' and resid 266 through 279 removed outlier: 3.731A pdb=" N THR R 270 " --> pdb=" O PRO R 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 288 removed outlier: 3.664A pdb=" N VAL R 287 " --> pdb=" O MET R 283 " (cutoff:3.500A) Processing helix chain 'R' and resid 292 through 300 Processing helix chain 'B' and resid 5 through 25 removed outlier: 3.593A pdb=" N CYS B 25 " --> pdb=" O ALA B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'G' and resid 9 through 24 removed outlier: 3.778A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 Processing helix chain 'G' and resid 45 through 48 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 8.921A pdb=" N ALA A 221 " --> pdb=" O GLU A 33 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N LYS A 35 " --> pdb=" O ALA A 221 " (cutoff:3.500A) removed outlier: 7.604A pdb=" N ILE A 223 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N LEU A 37 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N CYS A 225 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 39 " --> pdb=" O CYS A 225 " (cutoff:3.500A) removed outlier: 9.015A pdb=" N ALA A 227 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 5.840A pdb=" N ILE A 222 " --> pdb=" O ILE A 266 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N PHE A 268 " --> pdb=" O ILE A 222 " (cutoff:3.500A) removed outlier: 6.105A pdb=" N PHE A 224 " --> pdb=" O PHE A 268 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ASN A 270 " --> pdb=" O PHE A 224 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL A 226 " --> pdb=" O ASN A 270 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'R' and resid 74 through 76 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 51 removed outlier: 3.586A pdb=" N ARG B 49 " --> pdb=" O ILE B 338 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.590A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.611A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 100 through 105 removed outlier: 7.027A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 146 through 151 removed outlier: 3.648A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 187 through 192 removed outlier: 3.521A pdb=" N SER B 189 " --> pdb=" O GLY B 202 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.280A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 229 through 234 removed outlier: 6.497A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.773A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) 374 hydrogen bonds defined for protein. 1080 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: 1.99 Time building geometry restraints manager: 1.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1636 1.33 - 1.45: 1604 1.45 - 1.58: 3841 1.58 - 1.70: 0 1.70 - 1.83: 78 Bond restraints: 7159 Sorted by residual: bond pdb=" C VAL R 24 " pdb=" N PRO R 25 " ideal model delta sigma weight residual 1.334 1.403 -0.069 2.34e-02 1.83e+03 8.69e+00 bond pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " ideal model delta sigma weight residual 1.547 1.577 -0.030 1.68e-02 3.54e+03 3.29e+00 bond pdb=" C XTD R 402 " pdb=" C7 XTD R 402 " ideal model delta sigma weight residual 1.448 1.483 -0.035 2.00e-02 2.50e+03 3.11e+00 bond pdb=" CB ASP B 258 " pdb=" CG ASP B 258 " ideal model delta sigma weight residual 1.516 1.559 -0.043 2.50e-02 1.60e+03 2.92e+00 bond pdb=" CB PRO R 142 " pdb=" CG PRO R 142 " ideal model delta sigma weight residual 1.492 1.408 0.084 5.00e-02 4.00e+02 2.80e+00 ... (remaining 7154 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.73: 9458 2.73 - 5.45: 205 5.45 - 8.18: 32 8.18 - 10.91: 7 10.91 - 13.64: 2 Bond angle restraints: 9704 Sorted by residual: angle pdb=" CA CYS R 263 " pdb=" CB CYS R 263 " pdb=" SG CYS R 263 " ideal model delta sigma weight residual 114.40 124.77 -10.37 2.30e+00 1.89e-01 2.03e+01 angle pdb=" CA ILE G 28 " pdb=" CB ILE G 28 " pdb=" CG2 ILE G 28 " ideal model delta sigma weight residual 110.50 117.83 -7.33 1.70e+00 3.46e-01 1.86e+01 angle pdb=" CA CYS R 260 " pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " ideal model delta sigma weight residual 114.40 123.83 -9.43 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CA LEU B 318 " pdb=" CB LEU B 318 " pdb=" CG LEU B 318 " ideal model delta sigma weight residual 116.30 129.94 -13.64 3.50e+00 8.16e-02 1.52e+01 angle pdb=" CA LYS G 29 " pdb=" CB LYS G 29 " pdb=" CG LYS G 29 " ideal model delta sigma weight residual 114.10 106.36 7.74 2.00e+00 2.50e-01 1.50e+01 ... (remaining 9699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.42: 3900 16.42 - 32.84: 305 32.84 - 49.26: 71 49.26 - 65.68: 13 65.68 - 82.11: 4 Dihedral angle restraints: 4293 sinusoidal: 1703 harmonic: 2590 Sorted by residual: dihedral pdb=" CB CYS R 260 " pdb=" SG CYS R 260 " pdb=" SG CYS R 263 " pdb=" CB CYS R 263 " ideal model delta sinusoidal sigma weight residual -86.00 -43.23 -42.77 1 1.00e+01 1.00e-02 2.55e+01 dihedral pdb=" CA THR B 249 " pdb=" C THR B 249 " pdb=" N CYS B 250 " pdb=" CA CYS B 250 " ideal model delta harmonic sigma weight residual 180.00 158.04 21.96 0 5.00e+00 4.00e-02 1.93e+01 dihedral pdb=" CA GLN R 74 " pdb=" C GLN R 74 " pdb=" N THR R 75 " pdb=" CA THR R 75 " ideal model delta harmonic sigma weight residual 180.00 -160.18 -19.82 0 5.00e+00 4.00e-02 1.57e+01 ... (remaining 4290 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.112: 1028 0.112 - 0.224: 88 0.224 - 0.337: 1 0.337 - 0.449: 0 0.449 - 0.561: 1 Chirality restraints: 1118 Sorted by residual: chirality pdb=" CB VAL A 202 " pdb=" CA VAL A 202 " pdb=" CG1 VAL A 202 " pdb=" CG2 VAL A 202 " both_signs ideal model delta sigma weight residual False -2.63 -2.07 -0.56 2.00e-01 2.50e+01 7.87e+00 chirality pdb=" CB ILE G 9 " pdb=" CA ILE G 9 " pdb=" CG1 ILE G 9 " pdb=" CG2 ILE G 9 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB ILE G 28 " pdb=" CA ILE G 28 " pdb=" CG1 ILE G 28 " pdb=" CG2 ILE G 28 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1115 not shown) Planarity restraints: 1211 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C10 XTD R 402 " -0.047 2.00e-02 2.50e+03 2.89e-02 1.88e+01 pdb=" C11 XTD R 402 " 0.023 2.00e-02 2.50e+03 pdb=" C12 XTD R 402 " 0.029 2.00e-02 2.50e+03 pdb=" C13 XTD R 402 " 0.015 2.00e-02 2.50e+03 pdb=" C14 XTD R 402 " -0.037 2.00e-02 2.50e+03 pdb=" C15 XTD R 402 " 0.014 2.00e-02 2.50e+03 pdb=" C16 XTD R 402 " 0.013 2.00e-02 2.50e+03 pdb=" C17 XTD R 402 " -0.035 2.00e-02 2.50e+03 pdb=" C18 XTD R 402 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' ADN R 401 " -0.059 2.00e-02 2.50e+03 2.45e-02 1.65e+01 pdb=" C2 ADN R 401 " 0.008 2.00e-02 2.50e+03 pdb=" C4 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" C5 ADN R 401 " 0.012 2.00e-02 2.50e+03 pdb=" C6 ADN R 401 " -0.010 2.00e-02 2.50e+03 pdb=" C8 ADN R 401 " 0.020 2.00e-02 2.50e+03 pdb=" N1 ADN R 401 " -0.004 2.00e-02 2.50e+03 pdb=" N3 ADN R 401 " 0.022 2.00e-02 2.50e+03 pdb=" N6 ADN R 401 " -0.035 2.00e-02 2.50e+03 pdb=" N7 ADN R 401 " 0.016 2.00e-02 2.50e+03 pdb=" N9 ADN R 401 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR B 173 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C THR B 173 " 0.063 2.00e-02 2.50e+03 pdb=" O THR B 173 " -0.023 2.00e-02 2.50e+03 pdb=" N GLY B 174 " -0.022 2.00e-02 2.50e+03 ... (remaining 1208 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 1769 2.80 - 3.33: 6327 3.33 - 3.85: 11784 3.85 - 4.38: 14139 4.38 - 4.90: 24289 Nonbonded interactions: 58308 Sorted by model distance: nonbonded pdb=" O SER B 334 " pdb=" OG SER B 334 " model vdw 2.277 3.040 nonbonded pdb=" OG1 THR B 274 " pdb=" O VAL B 315 " model vdw 2.295 3.040 nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.312 3.040 nonbonded pdb=" O VAL R 138 " pdb=" OH TYR R 179 " model vdw 2.319 3.040 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.322 3.040 ... (remaining 58303 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: 1.570 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: 0.000 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.530 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 7161 Z= 0.271 Angle : 1.021 13.637 9708 Z= 0.566 Chirality : 0.063 0.561 1118 Planarity : 0.008 0.087 1211 Dihedral : 12.922 82.106 2603 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.13 % Allowed : 3.83 % Favored : 96.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.25), residues: 872 helix: -1.42 (0.22), residues: 404 sheet: 0.84 (0.38), residues: 173 loop : -1.24 (0.32), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP B 99 HIS 0.006 0.002 HIS A 323 PHE 0.042 0.003 PHE R 275 TYR 0.033 0.003 TYR A 297 ARG 0.012 0.001 ARG G 13 Details of bonding type rmsd hydrogen bonds : bond 0.22409 ( 374) hydrogen bonds : angle 7.74790 ( 1080) SS BOND : bond 0.00756 ( 2) SS BOND : angle 3.04824 ( 4) covalent geometry : bond 0.00619 ( 7159) covalent geometry : angle 1.01938 ( 9704) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 0.791 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8398 (m-80) cc_final: 0.7763 (m-80) REVERT: B 259 GLN cc_start: 0.8285 (pt0) cc_final: 0.7913 (pt0) outliers start: 1 outliers final: 0 residues processed: 121 average time/residue: 0.2051 time to fit residues: 33.0649 Evaluate side-chains 76 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.9980 chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 6.9990 chunk 22 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN A 332 ASN B 91 HIS B 132 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.168943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.137294 restraints weight = 7526.471| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 1.58 r_work: 0.3396 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7161 Z= 0.144 Angle : 0.589 7.981 9708 Z= 0.315 Chirality : 0.043 0.159 1118 Planarity : 0.005 0.063 1211 Dihedral : 6.924 54.655 995 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 1.06 % Allowed : 8.98 % Favored : 89.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.17 (0.28), residues: 872 helix: 0.21 (0.25), residues: 417 sheet: 0.51 (0.37), residues: 180 loop : -0.83 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.032 0.001 PHE R 275 TYR 0.012 0.001 TYR B 124 ARG 0.003 0.000 ARG B 8 Details of bonding type rmsd hydrogen bonds : bond 0.04326 ( 374) hydrogen bonds : angle 4.97530 ( 1080) SS BOND : bond 0.00372 ( 2) SS BOND : angle 1.91671 ( 4) covalent geometry : bond 0.00321 ( 7159) covalent geometry : angle 0.58772 ( 9704) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.774 Fit side-chains revert: symmetry clash REVERT: A 32 ARG cc_start: 0.8030 (ptt-90) cc_final: 0.7756 (ptp-170) REVERT: A 208 GLU cc_start: 0.7900 (pt0) cc_final: 0.7663 (pt0) REVERT: A 210 LYS cc_start: 0.9271 (ptmt) cc_final: 0.8952 (pttt) REVERT: B 101 MET cc_start: 0.8924 (mtp) cc_final: 0.8650 (mtp) REVERT: B 146 LEU cc_start: 0.8425 (OUTLIER) cc_final: 0.8143 (mp) outliers start: 8 outliers final: 4 residues processed: 94 average time/residue: 0.1952 time to fit residues: 25.1193 Evaluate side-chains 87 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 82 time to evaluate : 0.734 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain B residue 132 ASN Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 275 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.4980 chunk 82 optimal weight: 20.0000 chunk 35 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 81 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 80 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.167415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.136536 restraints weight = 7593.145| |-----------------------------------------------------------------------------| r_work (start): 0.3530 rms_B_bonded: 1.58 r_work: 0.3362 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3216 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7161 Z= 0.145 Angle : 0.543 7.103 9708 Z= 0.290 Chirality : 0.042 0.159 1118 Planarity : 0.004 0.054 1211 Dihedral : 6.272 52.941 995 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 9.64 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.21 (0.28), residues: 872 helix: 0.76 (0.26), residues: 413 sheet: 0.32 (0.36), residues: 179 loop : -0.77 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 82 HIS 0.003 0.001 HIS G 44 PHE 0.030 0.001 PHE R 275 TYR 0.016 0.001 TYR B 111 ARG 0.003 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03781 ( 374) hydrogen bonds : angle 4.70851 ( 1080) SS BOND : bond 0.00414 ( 2) SS BOND : angle 1.85210 ( 4) covalent geometry : bond 0.00334 ( 7159) covalent geometry : angle 0.54134 ( 9704) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 85 time to evaluate : 0.837 Fit side-chains REVERT: A 32 ARG cc_start: 0.8103 (ptt-90) cc_final: 0.7797 (ptp-170) REVERT: A 187 GLU cc_start: 0.7749 (mt-10) cc_final: 0.7535 (mt-10) REVERT: A 208 GLU cc_start: 0.7992 (pt0) cc_final: 0.7695 (pt0) REVERT: A 210 LYS cc_start: 0.9282 (ptmt) cc_final: 0.8943 (pttt) REVERT: B 146 LEU cc_start: 0.8399 (OUTLIER) cc_final: 0.8160 (mp) outliers start: 15 outliers final: 7 residues processed: 96 average time/residue: 0.1977 time to fit residues: 25.8252 Evaluate side-chains 86 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 78 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 6 optimal weight: 0.0030 chunk 77 optimal weight: 0.5980 chunk 29 optimal weight: 0.7980 chunk 78 optimal weight: 0.6980 chunk 86 optimal weight: 1.9990 chunk 46 optimal weight: 0.0020 overall best weight: 0.4198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.170711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138844 restraints weight = 7599.988| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 1.63 r_work: 0.3403 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 7161 Z= 0.106 Angle : 0.503 6.702 9708 Z= 0.270 Chirality : 0.041 0.149 1118 Planarity : 0.004 0.048 1211 Dihedral : 5.705 50.049 995 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.85 % Allowed : 10.57 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.54 (0.29), residues: 872 helix: 1.22 (0.27), residues: 409 sheet: 0.22 (0.36), residues: 176 loop : -0.70 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.002 0.001 HIS R 251 PHE 0.028 0.001 PHE R 275 TYR 0.014 0.001 TYR B 111 ARG 0.003 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03257 ( 374) hydrogen bonds : angle 4.44555 ( 1080) SS BOND : bond 0.00347 ( 2) SS BOND : angle 1.78116 ( 4) covalent geometry : bond 0.00231 ( 7159) covalent geometry : angle 0.50190 ( 9704) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.737 Fit side-chains REVERT: A 32 ARG cc_start: 0.8006 (ptt-90) cc_final: 0.7728 (ptp-170) REVERT: A 208 GLU cc_start: 0.7862 (pt0) cc_final: 0.7553 (pt0) REVERT: A 210 LYS cc_start: 0.9302 (ptmt) cc_final: 0.8937 (pttt) REVERT: R 29 LEU cc_start: 0.7721 (OUTLIER) cc_final: 0.7298 (mp) REVERT: B 13 GLN cc_start: 0.8392 (pp30) cc_final: 0.8174 (pp30) REVERT: B 101 MET cc_start: 0.8909 (mtp) cc_final: 0.8559 (mtp) outliers start: 14 outliers final: 8 residues processed: 93 average time/residue: 0.1965 time to fit residues: 24.8168 Evaluate side-chains 82 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 71 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 66 optimal weight: 8.9990 chunk 23 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 chunk 70 optimal weight: 3.9990 overall best weight: 1.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.162910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.128625 restraints weight = 7681.251| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.67 r_work: 0.3299 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3150 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7161 Z= 0.215 Angle : 0.571 6.805 9708 Z= 0.305 Chirality : 0.044 0.159 1118 Planarity : 0.004 0.050 1211 Dihedral : 6.022 53.253 995 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.25 % Allowed : 12.55 % Favored : 85.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.33 (0.29), residues: 872 helix: 1.11 (0.27), residues: 411 sheet: -0.06 (0.36), residues: 176 loop : -0.78 (0.37), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 82 HIS 0.004 0.001 HIS R 251 PHE 0.026 0.002 PHE R 275 TYR 0.013 0.001 TYR B 111 ARG 0.003 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03765 ( 374) hydrogen bonds : angle 4.60987 ( 1080) SS BOND : bond 0.00486 ( 2) SS BOND : angle 1.63364 ( 4) covalent geometry : bond 0.00512 ( 7159) covalent geometry : angle 0.57006 ( 9704) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 1.114 Fit side-chains REVERT: A 32 ARG cc_start: 0.8106 (ptt-90) cc_final: 0.7756 (ptp-170) REVERT: B 101 MET cc_start: 0.9096 (mtp) cc_final: 0.8827 (mtp) REVERT: B 197 ARG cc_start: 0.8320 (mtp85) cc_final: 0.8111 (mtp85) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.2519 time to fit residues: 31.3169 Evaluate side-chains 85 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 2.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 10.0000 chunk 38 optimal weight: 0.5980 chunk 26 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.5980 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 9 optimal weight: 6.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 205 GLN A 270 ASN ** R 147 ASN ** 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 = 0.3827 r_free = 0.3827 target = 0.163894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.129931 restraints weight = 7666.863| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.66 r_work: 0.3316 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3167 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.2595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7161 Z= 0.165 Angle : 0.539 6.655 9708 Z= 0.287 Chirality : 0.043 0.151 1118 Planarity : 0.004 0.048 1211 Dihedral : 5.875 51.673 995 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.64 % Allowed : 12.95 % Favored : 84.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.29), residues: 872 helix: 1.21 (0.27), residues: 411 sheet: -0.23 (0.37), residues: 181 loop : -0.76 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 82 HIS 0.003 0.001 HIS R 251 PHE 0.026 0.001 PHE R 275 TYR 0.014 0.001 TYR B 111 ARG 0.001 0.000 ARG B 150 Details of bonding type rmsd hydrogen bonds : bond 0.03502 ( 374) hydrogen bonds : angle 4.52078 ( 1080) SS BOND : bond 0.00431 ( 2) SS BOND : angle 1.68456 ( 4) covalent geometry : bond 0.00395 ( 7159) covalent geometry : angle 0.53771 ( 9704) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 77 time to evaluate : 1.055 Fit side-chains REVERT: A 32 ARG cc_start: 0.8119 (ptt-90) cc_final: 0.7775 (ptp-170) REVERT: A 296 LYS cc_start: 0.7913 (mppt) cc_final: 0.7584 (mmtt) outliers start: 20 outliers final: 17 residues processed: 92 average time/residue: 0.3049 time to fit residues: 37.8814 Evaluate side-chains 88 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 177 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 18 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 58 optimal weight: 0.0170 chunk 63 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 39 optimal weight: 0.0370 chunk 47 optimal weight: 0.0970 chunk 73 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 overall best weight: 0.3494 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.168292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.136381 restraints weight = 7532.158| |-----------------------------------------------------------------------------| r_work (start): 0.3531 rms_B_bonded: 1.56 r_work: 0.3388 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7161 Z= 0.101 Angle : 0.513 8.525 9708 Z= 0.269 Chirality : 0.041 0.140 1118 Planarity : 0.004 0.045 1211 Dihedral : 5.542 48.012 995 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.98 % Allowed : 14.53 % Favored : 83.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.68 (0.29), residues: 872 helix: 1.50 (0.27), residues: 409 sheet: 0.06 (0.38), residues: 173 loop : -0.74 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.006 0.001 HIS A 323 PHE 0.026 0.001 PHE R 275 TYR 0.006 0.001 TYR B 124 ARG 0.002 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 374) hydrogen bonds : angle 4.30451 ( 1080) SS BOND : bond 0.00332 ( 2) SS BOND : angle 1.71868 ( 4) covalent geometry : bond 0.00223 ( 7159) covalent geometry : angle 0.51213 ( 9704) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 1.025 Fit side-chains REVERT: A 277 GLU cc_start: 0.7569 (tp30) cc_final: 0.7297 (tp30) REVERT: A 296 LYS cc_start: 0.7770 (mppt) cc_final: 0.7483 (mmtt) REVERT: R 29 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7275 (mp) REVERT: B 55 LEU cc_start: 0.8819 (OUTLIER) cc_final: 0.8440 (mt) REVERT: B 101 MET cc_start: 0.8911 (mtp) cc_final: 0.8708 (mtp) outliers start: 15 outliers final: 8 residues processed: 85 average time/residue: 0.2569 time to fit residues: 29.7330 Evaluate side-chains 76 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 45 optimal weight: 0.7980 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 78 optimal weight: 0.9980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.164823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.133375 restraints weight = 7631.286| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 1.60 r_work: 0.3343 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3202 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3202 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 7161 Z= 0.156 Angle : 0.554 7.940 9708 Z= 0.289 Chirality : 0.042 0.140 1118 Planarity : 0.004 0.046 1211 Dihedral : 5.603 48.070 995 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.11 % Allowed : 14.53 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.52 (0.29), residues: 872 helix: 1.39 (0.27), residues: 414 sheet: -0.20 (0.38), residues: 177 loop : -0.75 (0.37), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 169 HIS 0.004 0.001 HIS B 54 PHE 0.024 0.001 PHE R 275 TYR 0.008 0.001 TYR B 111 ARG 0.003 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03290 ( 374) hydrogen bonds : angle 4.40349 ( 1080) SS BOND : bond 0.00432 ( 2) SS BOND : angle 1.58442 ( 4) covalent geometry : bond 0.00375 ( 7159) covalent geometry : angle 0.55277 ( 9704) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 73 time to evaluate : 0.766 Fit side-chains REVERT: A 277 GLU cc_start: 0.7664 (tp30) cc_final: 0.7381 (tp30) REVERT: A 290 GLU cc_start: 0.7492 (pm20) cc_final: 0.6934 (pm20) REVERT: A 296 LYS cc_start: 0.7848 (mppt) cc_final: 0.7551 (mmtt) REVERT: R 29 LEU cc_start: 0.7689 (OUTLIER) cc_final: 0.7348 (mp) REVERT: B 55 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8439 (mt) REVERT: B 101 MET cc_start: 0.8953 (mtp) cc_final: 0.8744 (mtp) outliers start: 16 outliers final: 12 residues processed: 86 average time/residue: 0.1870 time to fit residues: 22.1780 Evaluate side-chains 86 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 72 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 165 THR Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 43 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.5980 chunk 53 optimal weight: 0.9980 chunk 6 optimal weight: 0.0770 chunk 11 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 chunk 13 optimal weight: 0.0970 chunk 77 optimal weight: 3.9990 overall best weight: 0.5336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** R 147 ASN ** 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 = 0.3864 r_free = 0.3864 target = 0.167425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.135097 restraints weight = 7640.041| |-----------------------------------------------------------------------------| r_work (start): 0.3516 rms_B_bonded: 1.60 r_work: 0.3370 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7161 Z= 0.111 Angle : 0.555 14.717 9708 Z= 0.286 Chirality : 0.041 0.135 1118 Planarity : 0.004 0.044 1211 Dihedral : 5.461 45.981 995 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.98 % Allowed : 14.40 % Favored : 83.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.71 (0.29), residues: 872 helix: 1.57 (0.27), residues: 411 sheet: -0.15 (0.38), residues: 175 loop : -0.66 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 169 HIS 0.002 0.001 HIS R 251 PHE 0.025 0.001 PHE R 275 TYR 0.007 0.001 TYR B 264 ARG 0.002 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03036 ( 374) hydrogen bonds : angle 4.32675 ( 1080) SS BOND : bond 0.00811 ( 2) SS BOND : angle 5.25784 ( 4) covalent geometry : bond 0.00252 ( 7159) covalent geometry : angle 0.54444 ( 9704) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 73 time to evaluate : 0.808 Fit side-chains revert: symmetry clash REVERT: A 277 GLU cc_start: 0.7687 (tp30) cc_final: 0.7426 (tp30) REVERT: A 290 GLU cc_start: 0.7503 (pm20) cc_final: 0.6994 (pm20) REVERT: A 296 LYS cc_start: 0.7829 (mppt) cc_final: 0.7523 (mmtt) REVERT: R 29 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7262 (mp) REVERT: B 55 LEU cc_start: 0.8748 (OUTLIER) cc_final: 0.8389 (mt) REVERT: B 101 MET cc_start: 0.8996 (mtp) cc_final: 0.8758 (mtp) REVERT: B 164 THR cc_start: 0.8463 (p) cc_final: 0.8119 (p) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.2070 time to fit residues: 24.1326 Evaluate side-chains 84 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 71 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 270 ASN Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.2980 chunk 63 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3867 r_free = 0.3867 target = 0.167836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136564 restraints weight = 7747.232| |-----------------------------------------------------------------------------| r_work (start): 0.3545 rms_B_bonded: 1.57 r_work: 0.3375 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7161 Z= 0.113 Angle : 0.566 13.761 9708 Z= 0.290 Chirality : 0.041 0.138 1118 Planarity : 0.004 0.044 1211 Dihedral : 5.493 47.788 995 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 1.72 % Allowed : 14.93 % Favored : 83.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.77 (0.29), residues: 872 helix: 1.64 (0.27), residues: 411 sheet: -0.11 (0.38), residues: 175 loop : -0.65 (0.37), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 169 HIS 0.006 0.001 HIS A 323 PHE 0.024 0.001 PHE R 275 TYR 0.009 0.001 TYR B 111 ARG 0.002 0.000 ARG R 108 Details of bonding type rmsd hydrogen bonds : bond 0.03000 ( 374) hydrogen bonds : angle 4.31088 ( 1080) SS BOND : bond 0.00598 ( 2) SS BOND : angle 5.40323 ( 4) covalent geometry : bond 0.00261 ( 7159) covalent geometry : angle 0.55527 ( 9704) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1744 Ramachandran restraints generated. 872 Oldfield, 0 Emsley, 872 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.828 Fit side-chains revert: symmetry clash REVERT: A 51 LYS cc_start: 0.8899 (mptt) cc_final: 0.8673 (mmtt) REVERT: A 277 GLU cc_start: 0.7728 (tp30) cc_final: 0.7492 (tp30) REVERT: A 290 GLU cc_start: 0.7520 (pm20) cc_final: 0.7025 (pm20) REVERT: A 296 LYS cc_start: 0.7797 (mppt) cc_final: 0.7523 (mmtt) REVERT: R 29 LEU cc_start: 0.7680 (OUTLIER) cc_final: 0.7311 (mp) REVERT: R 143 MET cc_start: 0.7979 (mtm) cc_final: 0.7704 (mtp) REVERT: B 55 LEU cc_start: 0.8619 (OUTLIER) cc_final: 0.8243 (mt) REVERT: B 101 MET cc_start: 0.8988 (mtp) cc_final: 0.8760 (mtp) REVERT: B 164 THR cc_start: 0.8421 (p) cc_final: 0.8080 (p) outliers start: 13 outliers final: 11 residues processed: 87 average time/residue: 0.1941 time to fit residues: 23.5543 Evaluate side-chains 86 residues out of total 757 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 73 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 23 SER Chi-restraints excluded: chain R residue 29 LEU Chi-restraints excluded: chain R residue 104 ASP Chi-restraints excluded: chain R residue 225 TYR Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 184 THR Chi-restraints excluded: chain B residue 186 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain G residue 28 ILE Chi-restraints excluded: chain G residue 38 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 chunk 22 optimal weight: 0.6980 chunk 75 optimal weight: 6.9990 chunk 9 optimal weight: 1.9990 chunk 57 optimal weight: 4.9990 chunk 50 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 40 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 ASN ** R 147 ASN ** 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 = 0.3853 r_free = 0.3853 target = 0.166422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.132777 restraints weight = 7678.087| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 1.66 r_work: 0.3345 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7161 Z= 0.131 Angle : 0.559 12.121 9708 Z= 0.288 Chirality : 0.042 0.134 1118 Planarity : 0.004 0.045 1211 Dihedral : 5.490 46.541 995 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.11 % Allowed : 14.66 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.69 (0.29), residues: 872 helix: 1.57 (0.27), residues: 415 sheet: -0.23 (0.38), residues: 177 loop : -0.67 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 169 HIS 0.003 0.001 HIS R 251 PHE 0.023 0.001 PHE R 275 TYR 0.008 0.001 TYR B 264 ARG 0.001 0.000 ARG B 197 Details of bonding type rmsd hydrogen bonds : bond 0.03115 ( 374) hydrogen bonds : angle 4.31818 ( 1080) SS BOND : bond 0.00518 ( 2) SS BOND : angle 5.13537 ( 4) covalent geometry : bond 0.00312 ( 7159) covalent geometry : angle 0.54926 ( 9704) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4761.95 seconds wall clock time: 86 minutes 10.49 seconds (5170.49 seconds total)