Starting phenix.real_space_refine on Mon May 12 08:08:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpf_62486/05_2025/9kpf_62486.cif" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 65 5.16 5 C 5695 2.51 5 N 1499 2.21 5 O 1655 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8914 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1812 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1812 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 222} Chain breaks: 1 Chain: "B" Number of atoms: 2616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 341, 2616 Classifications: {'peptide': 341} Link IDs: {'PTRANS': 5, 'TRANS': 335} Chain: "G" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "R" Number of atoms: 2247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 272, 2247 Classifications: {'peptide': 272} Link IDs: {'PTRANS': 7, 'TRANS': 264} Chain breaks: 1 Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "R" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 20 Unusual residues: {'SA0': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.08, per 1000 atoms: 0.57 Number of scatterers: 8914 At special positions: 0 Unit cell: (93.12, 125.76, 124.8, 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 65 16.00 O 1655 8.00 N 1499 7.00 C 5695 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS R 69 " - pdb=" SG CYS R 79 " distance=2.03 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 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: 2.12 Conformation dependent library (CDL) restraints added in 970.7 milliseconds 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2118 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 12 sheets defined 37.6% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.89 Creating SS restraints... Processing helix chain 'A' and resid 6 through 32 removed outlier: 4.222A pdb=" N ARG A 32 " --> pdb=" O GLU A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 53 removed outlier: 3.989A pdb=" N ILE A 49 " --> pdb=" O GLY A 45 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N VAL A 50 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LYS A 51 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 53 " --> pdb=" O ILE A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 4.482A pdb=" N HIS A 213 " --> pdb=" O LYS A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 216 No H-bonds generated for 'chain 'A' and resid 214 through 216' Processing helix chain 'A' and resid 241 through 255 removed outlier: 3.738A pdb=" N ASN A 255 " --> pdb=" O ASP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 279 removed outlier: 3.811A pdb=" N LYS A 279 " --> pdb=" O GLU A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 286 removed outlier: 3.597A pdb=" N ILE A 285 " --> pdb=" O PRO A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 removed outlier: 3.883A pdb=" N LEU A 310 " --> pdb=" O GLN A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 351 removed outlier: 3.614A pdb=" N VAL A 332 " --> pdb=" O ASP A 328 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 removed outlier: 3.938A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.589A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 44 removed outlier: 4.026A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N HIS G 44 " --> pdb=" O TYR G 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 3 through 40 removed outlier: 3.927A pdb=" N THR R 7 " --> pdb=" O PRO R 3 " (cutoff:3.500A) Processing helix chain 'R' and resid 43 through 73 removed outlier: 3.587A pdb=" N MET R 47 " --> pdb=" O MET R 43 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP R 61 " --> pdb=" O PHE R 57 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 108 Processing helix chain 'R' and resid 112 through 125 Processing helix chain 'R' and resid 125 through 156 Proline residue: R 143 - end of helix Processing helix chain 'R' and resid 172 through 209 removed outlier: 3.801A pdb=" N ILE R 187 " --> pdb=" O VAL R 183 " (cutoff:3.500A) Proline residue: R 188 - end of helix removed outlier: 4.146A pdb=" N LEU R 191 " --> pdb=" O ILE R 187 " (cutoff:3.500A) Processing helix chain 'R' and resid 218 through 249 Processing helix chain 'R' and resid 258 through 279 Processing helix chain 'R' and resid 280 through 287 removed outlier: 3.502A pdb=" N LYS R 284 " --> pdb=" O SER R 280 " (cutoff:3.500A) Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.621A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 191 removed outlier: 3.690A pdb=" N ALA A 220 " --> pdb=" O LYS A 35 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N CYS A 224 " --> pdb=" O LEU A 39 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU A 268 " --> pdb=" O HIS A 322 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 46 through 51 removed outlier: 3.663A pdb=" N ARG B 46 " --> pdb=" O ASN B 340 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 5.086A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.024A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.257A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.970A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N GLY B 116 " --> pdb=" O ILE B 120 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N ILE B 120 " --> pdb=" O GLY B 116 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151 removed outlier: 7.182A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.849A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 5.423A pdb=" N PHE B 151 " --> pdb=" O GLN B 156 " (cutoff:3.500A) removed outlier: 7.585A pdb=" N GLN B 156 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N CYS B 166 " --> pdb=" O THR B 179 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N THR B 179 " --> pdb=" O CYS B 166 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.804A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.734A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.585A 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: 6.441A pdb=" N CYS B 250 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N THR B 263 " --> pdb=" O CYS B 250 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.682A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'S' and resid 3 through 7 removed outlier: 3.584A pdb=" N SER S 25 " --> pdb=" O GLN S 3 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER S 21 " --> pdb=" O SER S 7 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'S' and resid 10 through 12 removed outlier: 5.761A pdb=" N GLY S 10 " --> pdb=" O THR S 118 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N TRP S 36 " --> pdb=" O ALA S 49 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ALA S 49 " --> pdb=" O TRP S 36 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N ARG S 38 " --> pdb=" O TRP S 47 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N TRP S 47 " --> pdb=" O ARG S 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 134 through 136 removed outlier: 3.682A pdb=" N GLU S 234 " --> pdb=" O VAL S 135 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLY S 213 " --> pdb=" O LEU S 233 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ILE S 177 " --> pdb=" O TRP S 164 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N LEU S 166 " --> pdb=" O LEU S 175 " (cutoff:3.500A) removed outlier: 5.873A pdb=" N LEU S 175 " --> pdb=" O LEU S 166 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 143 through 147 removed outlier: 3.666A pdb=" N ALA S 199 " --> pdb=" O SER S 196 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1296 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: 2.44 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2840 1.34 - 1.46: 2233 1.46 - 1.58: 3939 1.58 - 1.70: 0 1.70 - 1.82: 95 Bond restraints: 9107 Sorted by residual: bond pdb=" N ILE R 286 " pdb=" CA ILE R 286 " ideal model delta sigma weight residual 1.461 1.492 -0.032 1.19e-02 7.06e+03 7.07e+00 bond pdb=" N ARG R 285 " pdb=" CA ARG R 285 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.19e-02 7.06e+03 5.53e+00 bond pdb=" N LYS R 284 " pdb=" CA LYS R 284 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.34e+00 bond pdb=" CB PRO G 60 " pdb=" CG PRO G 60 " ideal model delta sigma weight residual 1.492 1.570 -0.078 5.00e-02 4.00e+02 2.43e+00 bond pdb=" N LEU R 287 " pdb=" CA LEU R 287 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.90e-02 2.77e+03 2.42e+00 ... (remaining 9102 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.48: 11935 1.48 - 2.96: 310 2.96 - 4.44: 69 4.44 - 5.92: 14 5.92 - 7.40: 9 Bond angle restraints: 12337 Sorted by residual: angle pdb=" CA ARG B 19 " pdb=" CB ARG B 19 " pdb=" CG ARG B 19 " ideal model delta sigma weight residual 114.10 121.01 -6.91 2.00e+00 2.50e-01 1.19e+01 angle pdb=" CA PRO G 60 " pdb=" N PRO G 60 " pdb=" CD PRO G 60 " ideal model delta sigma weight residual 112.00 107.24 4.76 1.40e+00 5.10e-01 1.15e+01 angle pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " pdb=" CD GLN B 17 " ideal model delta sigma weight residual 112.60 118.24 -5.64 1.70e+00 3.46e-01 1.10e+01 angle pdb=" CA GLN B 17 " pdb=" CB GLN B 17 " pdb=" CG GLN B 17 " ideal model delta sigma weight residual 114.10 120.48 -6.38 2.00e+00 2.50e-01 1.02e+01 angle pdb=" C VAL A 201 " pdb=" CA VAL A 201 " pdb=" CB VAL A 201 " ideal model delta sigma weight residual 111.09 114.63 -3.54 1.11e+00 8.12e-01 1.01e+01 ... (remaining 12332 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.01: 4614 17.01 - 34.02: 607 34.02 - 51.03: 145 51.03 - 68.04: 25 68.04 - 85.05: 7 Dihedral angle restraints: 5398 sinusoidal: 2124 harmonic: 3274 Sorted by residual: dihedral pdb=" CB CYS R 69 " pdb=" SG CYS R 69 " pdb=" SG CYS R 79 " pdb=" CB CYS R 79 " ideal model delta sinusoidal sigma weight residual 93.00 36.05 56.95 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 159.78 20.22 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA MET S 93 " pdb=" C MET S 93 " pdb=" N TYR S 94 " pdb=" CA TYR S 94 " ideal model delta harmonic sigma weight residual -180.00 -162.29 -17.71 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 5395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 974 0.037 - 0.073: 310 0.073 - 0.110: 99 0.110 - 0.146: 20 0.146 - 0.183: 5 Chirality restraints: 1408 Sorted by residual: chirality pdb=" CA ILE R 286 " pdb=" N ILE R 286 " pdb=" C ILE R 286 " pdb=" CB ILE R 286 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.35e-01 chirality pdb=" CB THR R 242 " pdb=" CA THR R 242 " pdb=" OG1 THR R 242 " pdb=" CG2 THR R 242 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.17 2.00e-01 2.50e+01 7.29e-01 chirality pdb=" CA TYR S 223 " pdb=" N TYR S 223 " pdb=" C TYR S 223 " pdb=" CB TYR S 223 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.28e-01 ... (remaining 1405 not shown) Planarity restraints: 1543 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN G 59 " -0.070 5.00e-02 4.00e+02 1.04e-01 1.73e+01 pdb=" N PRO G 60 " 0.180 5.00e-02 4.00e+02 pdb=" CA PRO G 60 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO G 60 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR S 223 " 0.034 5.00e-02 4.00e+02 5.08e-02 4.12e+00 pdb=" N PRO S 224 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO S 224 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO S 224 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR S 138 " 0.027 5.00e-02 4.00e+02 4.18e-02 2.80e+00 pdb=" N PRO S 139 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO S 139 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO S 139 " 0.023 5.00e-02 4.00e+02 ... (remaining 1540 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 925 2.75 - 3.28: 8681 3.28 - 3.82: 14556 3.82 - 4.36: 16128 4.36 - 4.90: 28702 Nonbonded interactions: 68992 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O GLU B 130 " model vdw 2.208 3.040 nonbonded pdb=" OG SER S 133 " pdb=" N SER S 134 " model vdw 2.211 3.120 nonbonded pdb=" OD1 ASP B 247 " pdb=" OG1 THR B 249 " model vdw 2.225 3.040 nonbonded pdb=" OG1 THR B 86 " pdb=" ND2 ASN B 88 " model vdw 2.227 3.120 nonbonded pdb=" N GLY B 185 " pdb=" OD2 ASP B 205 " model vdw 2.272 3.120 ... (remaining 68987 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: 1.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 21.570 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.110 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 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 : 0.003 0.078 9110 Z= 0.153 Angle : 0.637 7.401 12343 Z= 0.351 Chirality : 0.041 0.183 1408 Planarity : 0.005 0.104 1543 Dihedral : 16.074 85.045 3271 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 0.10 % Allowed : 29.29 % Favored : 70.61 % 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: 0.89 (0.25), residues: 1111 helix: 2.48 (0.26), residues: 405 sheet: 0.51 (0.30), residues: 271 loop : -1.24 (0.28), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS R 209 PHE 0.021 0.001 PHE A 274 TYR 0.011 0.001 TYR S 95 ARG 0.007 0.000 ARG B 19 Details of bonding type rmsd hydrogen bonds : bond 0.11808 ( 447) hydrogen bonds : angle 5.01061 ( 1296) SS BOND : bond 0.00514 ( 3) SS BOND : angle 1.00734 ( 6) covalent geometry : bond 0.00313 ( 9107) covalent geometry : angle 0.63629 (12337) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.873 Fit side-chains revert: symmetry clash REVERT: B 290 ASP cc_start: 0.6525 (m-30) cc_final: 0.5774 (t70) REVERT: G 22 GLU cc_start: 0.7404 (mp0) cc_final: 0.7181 (mp0) outliers start: 1 outliers final: 0 residues processed: 183 average time/residue: 0.2315 time to fit residues: 56.3678 Evaluate side-chains 180 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 180 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.0980 chunk 84 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 87 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 52 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.157917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127982 restraints weight = 13149.401| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.58 r_work: 0.3553 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7089 moved from start: 0.0645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9110 Z= 0.127 Angle : 0.558 10.089 12343 Z= 0.294 Chirality : 0.040 0.165 1408 Planarity : 0.004 0.062 1543 Dihedral : 4.770 59.262 1238 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.96 % Allowed : 24.90 % Favored : 72.14 % 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: 1.00 (0.25), residues: 1111 helix: 2.59 (0.25), residues: 408 sheet: 0.65 (0.31), residues: 259 loop : -1.23 (0.28), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.016 0.001 PHE B 199 TYR 0.019 0.001 TYR R 266 ARG 0.003 0.000 ARG B 49 Details of bonding type rmsd hydrogen bonds : bond 0.05046 ( 447) hydrogen bonds : angle 4.30072 ( 1296) SS BOND : bond 0.00580 ( 3) SS BOND : angle 1.17385 ( 6) covalent geometry : bond 0.00276 ( 9107) covalent geometry : angle 0.55777 (12337) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 179 time to evaluate : 0.863 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7484 (tpt170) REVERT: B 258 ASP cc_start: 0.6073 (m-30) cc_final: 0.5807 (m-30) REVERT: B 290 ASP cc_start: 0.6506 (m-30) cc_final: 0.5144 (t70) REVERT: R 121 ARG cc_start: 0.7304 (OUTLIER) cc_final: 0.7016 (mtt-85) REVERT: S 27 PHE cc_start: 0.8224 (OUTLIER) cc_final: 0.7785 (p90) outliers start: 29 outliers final: 15 residues processed: 195 average time/residue: 0.2515 time to fit residues: 64.7796 Evaluate side-chains 193 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 176 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ILE Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 251 LEU Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 143 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 58 optimal weight: 4.9990 chunk 18 optimal weight: 0.0570 chunk 89 optimal weight: 0.9990 chunk 81 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 64 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 46 optimal weight: 3.9990 overall best weight: 1.5304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 130 GLN ** 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 = 0.4010 r_free = 0.4010 target = 0.153712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.123948 restraints weight = 13279.083| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.59 r_work: 0.3489 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 9110 Z= 0.247 Angle : 0.659 10.762 12343 Z= 0.350 Chirality : 0.044 0.223 1408 Planarity : 0.005 0.055 1543 Dihedral : 5.192 60.827 1238 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 5.71 % Allowed : 23.16 % Favored : 71.12 % 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: 0.62 (0.25), residues: 1111 helix: 2.19 (0.25), residues: 408 sheet: 0.39 (0.30), residues: 278 loop : -1.39 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP R 261 HIS 0.006 0.002 HIS B 54 PHE 0.025 0.002 PHE B 199 TYR 0.018 0.003 TYR S 223 ARG 0.007 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.06693 ( 447) hydrogen bonds : angle 4.62045 ( 1296) SS BOND : bond 0.00764 ( 3) SS BOND : angle 1.37353 ( 6) covalent geometry : bond 0.00574 ( 9107) covalent geometry : angle 0.65842 (12337) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 195 time to evaluate : 0.916 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7688 (OUTLIER) cc_final: 0.7480 (mtmm) REVERT: A 28 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6964 (tt0) REVERT: B 258 ASP cc_start: 0.6108 (m-30) cc_final: 0.5834 (m-30) REVERT: R 67 ASN cc_start: 0.6890 (m110) cc_final: 0.6677 (m110) REVERT: R 121 ARG cc_start: 0.7249 (OUTLIER) cc_final: 0.6977 (mtt-85) REVERT: R 242 THR cc_start: 0.7801 (t) cc_final: 0.7575 (m) REVERT: S 27 PHE cc_start: 0.8205 (OUTLIER) cc_final: 0.7793 (p90) REVERT: S 155 HIS cc_start: 0.8201 (t-90) cc_final: 0.7903 (t-90) outliers start: 56 outliers final: 32 residues processed: 223 average time/residue: 0.2430 time to fit residues: 72.0895 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 193 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 LYS Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 325 CYS Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 219 MET Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 160 THR Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 211 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 2.9990 chunk 79 optimal weight: 0.6980 chunk 13 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 95 optimal weight: 0.0980 chunk 59 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 14 optimal weight: 2.9990 chunk 88 optimal weight: 0.0670 chunk 65 optimal weight: 0.9990 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.157253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.127380 restraints weight = 13143.270| |-----------------------------------------------------------------------------| r_work (start): 0.3664 rms_B_bonded: 2.59 r_work: 0.3541 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7101 moved from start: 0.1237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9110 Z= 0.120 Angle : 0.553 8.860 12343 Z= 0.289 Chirality : 0.040 0.174 1408 Planarity : 0.004 0.050 1543 Dihedral : 4.886 59.127 1238 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 4.69 % Allowed : 25.00 % Favored : 70.31 % 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: 0.97 (0.25), residues: 1111 helix: 2.59 (0.25), residues: 409 sheet: 0.49 (0.30), residues: 275 loop : -1.27 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS B 225 PHE 0.017 0.001 PHE R 9 TYR 0.019 0.001 TYR R 266 ARG 0.003 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.04841 ( 447) hydrogen bonds : angle 4.21075 ( 1296) SS BOND : bond 0.00515 ( 3) SS BOND : angle 0.97395 ( 6) covalent geometry : bond 0.00253 ( 9107) covalent geometry : angle 0.55259 (12337) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 188 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5883 (OUTLIER) cc_final: 0.5636 (mt-10) REVERT: A 28 GLU cc_start: 0.7157 (OUTLIER) cc_final: 0.6807 (tt0) REVERT: B 217 MET cc_start: 0.7993 (OUTLIER) cc_final: 0.7345 (pmm) REVERT: B 259 GLN cc_start: 0.8149 (pm20) cc_final: 0.7937 (pm20) REVERT: R 43 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5923 (pmm) REVERT: R 67 ASN cc_start: 0.6861 (m110) cc_final: 0.6615 (m110) REVERT: R 121 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6938 (mtt-85) REVERT: R 200 MET cc_start: 0.7160 (mtt) cc_final: 0.6761 (mmm) REVERT: R 242 THR cc_start: 0.7853 (t) cc_final: 0.7557 (m) REVERT: S 143 VAL cc_start: 0.7688 (OUTLIER) cc_final: 0.7420 (m) REVERT: S 155 HIS cc_start: 0.8141 (t-90) cc_final: 0.7910 (t-90) outliers start: 46 outliers final: 21 residues processed: 215 average time/residue: 0.2356 time to fit residues: 67.2987 Evaluate side-chains 211 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 184 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 130 GLN Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 210 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 GLN B 155 ASN ** R 112 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 = 0.4004 r_free = 0.4004 target = 0.153184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3619 r_free = 0.3619 target = 0.123727 restraints weight = 13094.137| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.57 r_work: 0.3485 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3485 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 9110 Z= 0.250 Angle : 0.660 10.099 12343 Z= 0.348 Chirality : 0.044 0.228 1408 Planarity : 0.005 0.052 1543 Dihedral : 5.249 62.149 1238 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 5.00 % Allowed : 25.31 % Favored : 69.69 % 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: 0.61 (0.25), residues: 1111 helix: 2.24 (0.25), residues: 406 sheet: 0.29 (0.29), residues: 278 loop : -1.37 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP R 261 HIS 0.005 0.001 HIS A 213 PHE 0.025 0.002 PHE B 199 TYR 0.022 0.002 TYR S 223 ARG 0.005 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.06570 ( 447) hydrogen bonds : angle 4.56019 ( 1296) SS BOND : bond 0.00783 ( 3) SS BOND : angle 1.33492 ( 6) covalent geometry : bond 0.00583 ( 9107) covalent geometry : angle 0.65931 (12337) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 197 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7357 (OUTLIER) cc_final: 0.7006 (tt0) REVERT: B 163 ASP cc_start: 0.6891 (t0) cc_final: 0.6660 (t0) REVERT: B 217 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7289 (pmm) REVERT: B 258 ASP cc_start: 0.6424 (m-30) cc_final: 0.6109 (m-30) REVERT: B 259 GLN cc_start: 0.8034 (pm20) cc_final: 0.7821 (pm20) REVERT: R 43 MET cc_start: 0.6424 (OUTLIER) cc_final: 0.6087 (pmm) REVERT: R 67 ASN cc_start: 0.6898 (m110) cc_final: 0.6603 (m110) REVERT: R 121 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6831 (mtt-85) REVERT: R 200 MET cc_start: 0.7253 (mtt) cc_final: 0.6786 (mmm) REVERT: R 242 THR cc_start: 0.7853 (t) cc_final: 0.7478 (m) REVERT: R 246 THR cc_start: 0.6278 (OUTLIER) cc_final: 0.5657 (m) REVERT: S 27 PHE cc_start: 0.8245 (OUTLIER) cc_final: 0.7841 (p90) REVERT: S 155 HIS cc_start: 0.8251 (t-90) cc_final: 0.7981 (t-90) outliers start: 49 outliers final: 38 residues processed: 223 average time/residue: 0.2224 time to fit residues: 66.3892 Evaluate side-chains 240 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 196 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 68 ARG Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 233 CYS Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 139 VAL Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 271 MET Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 27 PHE Chi-restraints excluded: chain S residue 69 THR Chi-restraints excluded: chain S residue 116 THR Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 211 ASP Chi-restraints excluded: chain S residue 221 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.5980 chunk 34 optimal weight: 0.9990 chunk 50 optimal weight: 0.0670 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 86 optimal weight: 3.9990 chunk 75 optimal weight: 0.1980 chunk 64 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 130 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.155955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126108 restraints weight = 13169.331| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.59 r_work: 0.3519 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9110 Z= 0.131 Angle : 0.578 9.655 12343 Z= 0.300 Chirality : 0.041 0.191 1408 Planarity : 0.004 0.049 1543 Dihedral : 4.982 59.991 1238 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.00 % Allowed : 26.12 % Favored : 68.88 % 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: 0.90 (0.25), residues: 1111 helix: 2.54 (0.25), residues: 407 sheet: 0.38 (0.30), residues: 277 loop : -1.24 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.018 0.001 PHE B 199 TYR 0.018 0.001 TYR R 266 ARG 0.002 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.05128 ( 447) hydrogen bonds : angle 4.25542 ( 1296) SS BOND : bond 0.00593 ( 3) SS BOND : angle 0.99751 ( 6) covalent geometry : bond 0.00287 ( 9107) covalent geometry : angle 0.57783 (12337) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 186 time to evaluate : 0.979 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6037 (OUTLIER) cc_final: 0.5747 (mt-10) REVERT: B 217 MET cc_start: 0.7953 (OUTLIER) cc_final: 0.7291 (pmm) REVERT: B 258 ASP cc_start: 0.6387 (m-30) cc_final: 0.6084 (m-30) REVERT: B 259 GLN cc_start: 0.8137 (pm20) cc_final: 0.7926 (pm20) REVERT: R 43 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5930 (pmm) REVERT: R 67 ASN cc_start: 0.6877 (m110) cc_final: 0.6548 (m110) REVERT: R 121 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6904 (mtt-85) REVERT: R 135 MET cc_start: 0.7125 (OUTLIER) cc_final: 0.6834 (ttm) REVERT: R 186 VAL cc_start: 0.7538 (OUTLIER) cc_final: 0.7036 (t) REVERT: R 200 MET cc_start: 0.7237 (mtt) cc_final: 0.6763 (mmm) REVERT: R 242 THR cc_start: 0.7881 (t) cc_final: 0.7584 (m) REVERT: S 155 HIS cc_start: 0.8213 (t-90) cc_final: 0.7983 (t-90) REVERT: S 232 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7293 (tmtt) outliers start: 49 outliers final: 31 residues processed: 212 average time/residue: 0.2352 time to fit residues: 66.5181 Evaluate side-chains 224 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 186 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 232 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 15 optimal weight: 0.4980 chunk 26 optimal weight: 0.5980 chunk 4 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN R 67 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.155879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.125960 restraints weight = 13221.955| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 2.60 r_work: 0.3516 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 9110 Z= 0.143 Angle : 0.592 9.069 12343 Z= 0.307 Chirality : 0.041 0.188 1408 Planarity : 0.004 0.053 1543 Dihedral : 4.987 60.749 1238 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.80 % Allowed : 26.02 % Favored : 69.18 % 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: 0.89 (0.25), residues: 1111 helix: 2.56 (0.25), residues: 407 sheet: 0.36 (0.30), residues: 277 loop : -1.26 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.019 0.001 PHE B 199 TYR 0.016 0.002 TYR S 223 ARG 0.002 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.05100 ( 447) hydrogen bonds : angle 4.22450 ( 1296) SS BOND : bond 0.00568 ( 3) SS BOND : angle 1.37598 ( 6) covalent geometry : bond 0.00321 ( 9107) covalent geometry : angle 0.59151 (12337) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 187 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6098 (OUTLIER) cc_final: 0.5788 (mt-10) REVERT: B 217 MET cc_start: 0.7948 (OUTLIER) cc_final: 0.7288 (pmm) REVERT: B 258 ASP cc_start: 0.6380 (m-30) cc_final: 0.6077 (m-30) REVERT: B 259 GLN cc_start: 0.8126 (pm20) cc_final: 0.7894 (pm20) REVERT: R 43 MET cc_start: 0.6276 (OUTLIER) cc_final: 0.5934 (pmm) REVERT: R 121 ARG cc_start: 0.7193 (OUTLIER) cc_final: 0.6914 (mtt-85) REVERT: R 135 MET cc_start: 0.7168 (OUTLIER) cc_final: 0.6858 (ttm) REVERT: R 200 MET cc_start: 0.7194 (mtt) cc_final: 0.6732 (mmm) REVERT: S 143 VAL cc_start: 0.7693 (OUTLIER) cc_final: 0.7456 (m) REVERT: S 155 HIS cc_start: 0.8201 (t-90) cc_final: 0.7958 (t-90) REVERT: S 232 LYS cc_start: 0.7723 (OUTLIER) cc_final: 0.7419 (tmtt) outliers start: 47 outliers final: 33 residues processed: 209 average time/residue: 0.2387 time to fit residues: 66.5353 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 189 time to evaluate : 0.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 38 MET Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 219 MET Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 232 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 69 optimal weight: 0.5980 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.0470 chunk 90 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 75 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 74 optimal weight: 0.5980 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.156853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126789 restraints weight = 13358.690| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.62 r_work: 0.3528 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7119 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9110 Z= 0.125 Angle : 0.571 8.792 12343 Z= 0.296 Chirality : 0.041 0.272 1408 Planarity : 0.004 0.051 1543 Dihedral : 4.897 60.651 1238 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.98 % Allowed : 26.73 % Favored : 69.29 % 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: 0.96 (0.26), residues: 1111 helix: 2.70 (0.25), residues: 407 sheet: 0.38 (0.30), residues: 272 loop : -1.29 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.017 0.001 PHE B 199 TYR 0.019 0.001 TYR R 266 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04680 ( 447) hydrogen bonds : angle 4.15273 ( 1296) SS BOND : bond 0.00503 ( 3) SS BOND : angle 1.12610 ( 6) covalent geometry : bond 0.00278 ( 9107) covalent geometry : angle 0.57101 (12337) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 199 time to evaluate : 0.959 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5919 (OUTLIER) cc_final: 0.5653 (mt-10) REVERT: A 10 LYS cc_start: 0.7326 (mtmm) cc_final: 0.7059 (mtmm) REVERT: A 24 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.7336 (mtp-110) REVERT: A 28 GLU cc_start: 0.7122 (OUTLIER) cc_final: 0.6683 (tt0) REVERT: A 243 MET cc_start: 0.6616 (tpp) cc_final: 0.6336 (tpp) REVERT: B 217 MET cc_start: 0.7949 (OUTLIER) cc_final: 0.7294 (pmm) REVERT: B 259 GLN cc_start: 0.8121 (pm20) cc_final: 0.7876 (pm20) REVERT: B 314 ARG cc_start: 0.7295 (mtt180) cc_final: 0.7063 (ttt180) REVERT: G 22 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7074 (mp0) REVERT: R 43 MET cc_start: 0.6234 (OUTLIER) cc_final: 0.5900 (pmm) REVERT: R 105 ILE cc_start: 0.7345 (tt) cc_final: 0.7096 (mm) REVERT: R 121 ARG cc_start: 0.7190 (OUTLIER) cc_final: 0.6896 (mtt-85) REVERT: R 135 MET cc_start: 0.7100 (OUTLIER) cc_final: 0.6809 (ttm) REVERT: R 200 MET cc_start: 0.7154 (mtt) cc_final: 0.6670 (mmm) REVERT: S 143 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7431 (m) REVERT: S 232 LYS cc_start: 0.7718 (OUTLIER) cc_final: 0.7376 (tmtt) outliers start: 39 outliers final: 29 residues processed: 215 average time/residue: 0.2398 time to fit residues: 68.4614 Evaluate side-chains 231 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 193 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 8 GLU Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 135 MET Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 232 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 5.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 125 ASN B 155 ASN ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4036 r_free = 0.4036 target = 0.155847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.125753 restraints weight = 13262.946| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.62 r_work: 0.3507 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9110 Z= 0.163 Angle : 0.608 9.084 12343 Z= 0.317 Chirality : 0.042 0.276 1408 Planarity : 0.004 0.053 1543 Dihedral : 5.008 61.601 1238 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.39 % Allowed : 26.53 % Favored : 69.08 % 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: 0.85 (0.25), residues: 1111 helix: 2.58 (0.25), residues: 407 sheet: 0.32 (0.30), residues: 277 loop : -1.33 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.007 0.001 HIS S 155 PHE 0.022 0.002 PHE B 199 TYR 0.016 0.002 TYR R 266 ARG 0.004 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.05229 ( 447) hydrogen bonds : angle 4.26547 ( 1296) SS BOND : bond 0.00572 ( 3) SS BOND : angle 1.35948 ( 6) covalent geometry : bond 0.00375 ( 9107) covalent geometry : angle 0.60768 (12337) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.896 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7429 (mtmm) cc_final: 0.7129 (mtmm) REVERT: A 28 GLU cc_start: 0.7160 (OUTLIER) cc_final: 0.6709 (tt0) REVERT: A 243 MET cc_start: 0.6641 (tpp) cc_final: 0.6369 (tpp) REVERT: B 19 ARG cc_start: 0.7725 (tpt170) cc_final: 0.7442 (tpt170) REVERT: B 217 MET cc_start: 0.7947 (OUTLIER) cc_final: 0.7287 (pmm) REVERT: B 259 GLN cc_start: 0.8099 (pm20) cc_final: 0.7853 (pm20) REVERT: B 291 ASP cc_start: 0.7033 (m-30) cc_final: 0.6815 (m-30) REVERT: B 314 ARG cc_start: 0.7363 (mtt180) cc_final: 0.6982 (tpp80) REVERT: G 22 GLU cc_start: 0.7353 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: R 43 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5901 (pmm) REVERT: R 121 ARG cc_start: 0.7218 (OUTLIER) cc_final: 0.6920 (mtt-85) REVERT: R 200 MET cc_start: 0.7175 (mtt) cc_final: 0.6705 (mmm) REVERT: S 143 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7268 (m) REVERT: S 232 LYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7332 (tmtt) outliers start: 43 outliers final: 34 residues processed: 211 average time/residue: 0.2402 time to fit residues: 67.1317 Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 28 GLU Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 207 GLU Chi-restraints excluded: chain A residue 247 MET Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 171 ILE Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 47 MET Chi-restraints excluded: chain R residue 50 ILE Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 186 VAL Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 148 ARG Chi-restraints excluded: chain S residue 232 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 51 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 48 optimal weight: 0.2980 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 0.5980 chunk 100 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 38 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 112 HIS ** 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 = 0.4049 r_free = 0.4049 target = 0.156928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.126815 restraints weight = 13159.952| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.59 r_work: 0.3527 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7125 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9110 Z= 0.135 Angle : 0.598 8.900 12343 Z= 0.312 Chirality : 0.041 0.257 1408 Planarity : 0.004 0.051 1543 Dihedral : 4.939 60.774 1238 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 3.67 % Allowed : 27.35 % Favored : 68.98 % 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: 0.90 (0.25), residues: 1111 helix: 2.69 (0.25), residues: 407 sheet: 0.34 (0.30), residues: 272 loop : -1.35 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.018 0.001 PHE B 199 TYR 0.017 0.002 TYR R 266 ARG 0.003 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04800 ( 447) hydrogen bonds : angle 4.18920 ( 1296) SS BOND : bond 0.00541 ( 3) SS BOND : angle 1.18854 ( 6) covalent geometry : bond 0.00302 ( 9107) covalent geometry : angle 0.59776 (12337) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2222 Ramachandran restraints generated. 1111 Oldfield, 0 Emsley, 1111 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.946 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7347 (mtmm) cc_final: 0.7043 (mtmm) REVERT: A 24 ARG cc_start: 0.7538 (mtp-110) cc_final: 0.7324 (mtp-110) REVERT: A 216 GLU cc_start: 0.7575 (tm-30) cc_final: 0.7343 (tm-30) REVERT: B 19 ARG cc_start: 0.7717 (tpt170) cc_final: 0.7399 (tpt170) REVERT: B 217 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.7280 (pmm) REVERT: B 259 GLN cc_start: 0.8101 (pm20) cc_final: 0.7860 (pm20) REVERT: B 314 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6935 (tpp80) REVERT: G 22 GLU cc_start: 0.7345 (OUTLIER) cc_final: 0.7061 (mp0) REVERT: R 43 MET cc_start: 0.6222 (OUTLIER) cc_final: 0.5888 (pmm) REVERT: R 105 ILE cc_start: 0.7363 (tt) cc_final: 0.7102 (mm) REVERT: R 121 ARG cc_start: 0.7201 (OUTLIER) cc_final: 0.6897 (mtt-85) REVERT: R 200 MET cc_start: 0.7150 (mtt) cc_final: 0.6686 (mmm) REVERT: S 143 VAL cc_start: 0.7661 (OUTLIER) cc_final: 0.7271 (m) REVERT: S 232 LYS cc_start: 0.7727 (OUTLIER) cc_final: 0.7418 (tmtt) outliers start: 36 outliers final: 27 residues processed: 209 average time/residue: 0.2393 time to fit residues: 65.9160 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 190 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 GLU Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 32 ARG Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 344 ILE Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 173 THR Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 22 GLU Chi-restraints excluded: chain G residue 54 VAL Chi-restraints excluded: chain R residue 43 MET Chi-restraints excluded: chain R residue 82 THR Chi-restraints excluded: chain R residue 101 VAL Chi-restraints excluded: chain R residue 104 CYS Chi-restraints excluded: chain R residue 121 ARG Chi-restraints excluded: chain R residue 138 CYS Chi-restraints excluded: chain R residue 196 THR Chi-restraints excluded: chain R residue 205 LYS Chi-restraints excluded: chain R residue 208 GLN Chi-restraints excluded: chain R residue 246 THR Chi-restraints excluded: chain R residue 279 SER Chi-restraints excluded: chain S residue 2 VAL Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 210 GLU Chi-restraints excluded: chain S residue 232 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 53 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.0470 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 71 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 85 optimal weight: 0.0030 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 overall best weight: 0.3288 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN B 75 GLN B 239 ASN B 295 ASN ** R 112 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.158939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.128791 restraints weight = 13256.529| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.61 r_work: 0.3554 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7100 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 9110 Z= 0.111 Angle : 0.564 8.370 12343 Z= 0.293 Chirality : 0.040 0.233 1408 Planarity : 0.003 0.052 1543 Dihedral : 4.804 59.623 1238 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.27 % Allowed : 27.96 % Favored : 68.78 % 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: 1.08 (0.26), residues: 1111 helix: 2.90 (0.25), residues: 406 sheet: 0.44 (0.30), residues: 270 loop : -1.32 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.005 0.001 HIS A 188 PHE 0.015 0.001 PHE R 126 TYR 0.020 0.001 TYR R 266 ARG 0.002 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.04055 ( 447) hydrogen bonds : angle 4.04461 ( 1296) SS BOND : bond 0.00460 ( 3) SS BOND : angle 0.95062 ( 6) covalent geometry : bond 0.00241 ( 9107) covalent geometry : angle 0.56366 (12337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4423.47 seconds wall clock time: 77 minutes 31.06 seconds (4651.06 seconds total)