Starting phenix.real_space_refine on Sat Jun 7 15:55:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpf_62486/06_2025/9kpf_62486.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpf_62486/06_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_62486/06_2025/9kpf_62486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpf_62486/06_2025/9kpf_62486.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpf_62486/06_2025/9kpf_62486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpf_62486/06_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-5710/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: 5.56, per 1000 atoms: 0.62 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: 2.38 Conformation dependent library (CDL) restraints added in 967.2 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: 1.05 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: 2.74 Time building geometry restraints manager: 2.75 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.250 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.440 ------------------------------------------------------------------------------- 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 : 0.955 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: 0.2373 time to fit residues: 57.8270 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 : 0.976 ------------------------------------------------------------------------------- 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 = 44)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.127986 restraints weight = 13149.402| |-----------------------------------------------------------------------------| r_work (start): 0.3679 rms_B_bonded: 2.58 r_work: 0.3552 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 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 : 0.880 Fit side-chains revert: symmetry clash REVERT: B 19 ARG cc_start: 0.7693 (tpt170) cc_final: 0.7483 (tpt170) REVERT: B 258 ASP cc_start: 0.6074 (m-30) cc_final: 0.5808 (m-30) REVERT: B 290 ASP cc_start: 0.6508 (m-30) cc_final: 0.5148 (t70) REVERT: R 121 ARG cc_start: 0.7309 (OUTLIER) cc_final: 0.7021 (mtt-85) REVERT: S 27 PHE cc_start: 0.8225 (OUTLIER) cc_final: 0.7785 (p90) outliers start: 29 outliers final: 15 residues processed: 195 average time/residue: 0.2465 time to fit residues: 63.4159 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 : 0.892 ------------------------------------------------------------------------------- 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: 3.9990 chunk 81 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 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: 2.9990 overall best weight: 1.7304 ------------------------------------------------------------------------------- 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 = 0.4005 r_free = 0.4005 target = 0.153272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.123506 restraints weight = 13289.644| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 2.60 r_work: 0.3483 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3483 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 9110 Z= 0.276 Angle : 0.679 10.991 12343 Z= 0.361 Chirality : 0.045 0.230 1408 Planarity : 0.005 0.056 1543 Dihedral : 5.246 61.192 1238 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 5.92 % Allowed : 23.16 % Favored : 70.92 % 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: 0.55 (0.25), residues: 1111 helix: 2.12 (0.25), residues: 408 sheet: 0.36 (0.29), residues: 278 loop : -1.41 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP R 261 HIS 0.006 0.002 HIS A 213 PHE 0.027 0.002 PHE B 199 TYR 0.020 0.003 TYR S 223 ARG 0.010 0.001 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.06918 ( 447) hydrogen bonds : angle 4.67710 ( 1296) SS BOND : bond 0.00802 ( 3) SS BOND : angle 1.42797 ( 6) covalent geometry : bond 0.00643 ( 9107) covalent geometry : angle 0.67796 (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 254 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 196 time to evaluate : 0.990 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7710 (OUTLIER) cc_final: 0.7498 (mtmm) REVERT: A 28 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6983 (tt0) REVERT: A 51 LYS cc_start: 0.7893 (pttt) cc_final: 0.7660 (pttt) REVERT: B 258 ASP cc_start: 0.6126 (m-30) cc_final: 0.5849 (m-30) REVERT: R 67 ASN cc_start: 0.6908 (m110) cc_final: 0.6691 (m110) REVERT: R 121 ARG cc_start: 0.7248 (OUTLIER) cc_final: 0.6977 (mtt-85) REVERT: R 242 THR cc_start: 0.7834 (t) cc_final: 0.7596 (t) REVERT: S 27 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7806 (p90) REVERT: S 155 HIS cc_start: 0.8208 (t-90) cc_final: 0.7903 (t-90) outliers start: 58 outliers final: 34 residues processed: 227 average time/residue: 0.2411 time to fit residues: 73.0869 Evaluate side-chains 233 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 195 time to evaluate : 0.948 ------------------------------------------------------------------------------- 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 233 CYS 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 Chi-restraints excluded: chain S residue 221 LEU 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: 0.2980 chunk 13 optimal weight: 0.6980 chunk 45 optimal weight: 0.8980 chunk 95 optimal weight: 0.4980 chunk 59 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 88 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.156408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.126511 restraints weight = 13122.721| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 2.59 r_work: 0.3528 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.3528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9110 Z= 0.132 Angle : 0.569 9.200 12343 Z= 0.298 Chirality : 0.040 0.187 1408 Planarity : 0.004 0.050 1543 Dihedral : 4.954 59.355 1238 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 5.41 % Allowed : 24.18 % Favored : 70.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.25), residues: 1111 helix: 2.48 (0.25), residues: 410 sheet: 0.42 (0.30), residues: 276 loop : -1.32 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 169 HIS 0.003 0.001 HIS B 225 PHE 0.018 0.001 PHE B 199 TYR 0.018 0.002 TYR R 266 ARG 0.004 0.000 ARG B 314 Details of bonding type rmsd hydrogen bonds : bond 0.05188 ( 447) hydrogen bonds : angle 4.29132 ( 1296) SS BOND : bond 0.00564 ( 3) SS BOND : angle 1.04252 ( 6) covalent geometry : bond 0.00289 ( 9107) covalent geometry : angle 0.56844 (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 239 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 186 time to evaluate : 0.887 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6013 (OUTLIER) cc_final: 0.5746 (mt-10) REVERT: A 28 GLU cc_start: 0.7197 (OUTLIER) cc_final: 0.6839 (tt0) REVERT: A 51 LYS cc_start: 0.7879 (pttt) cc_final: 0.7662 (pttt) REVERT: B 217 MET cc_start: 0.8012 (OUTLIER) cc_final: 0.7306 (pmm) REVERT: B 259 GLN cc_start: 0.8135 (pm20) cc_final: 0.7923 (pm20) REVERT: G 22 GLU cc_start: 0.7381 (OUTLIER) cc_final: 0.7079 (mp0) REVERT: R 43 MET cc_start: 0.6282 (OUTLIER) cc_final: 0.5924 (pmm) REVERT: R 67 ASN cc_start: 0.6859 (m110) cc_final: 0.6597 (m110) REVERT: R 121 ARG cc_start: 0.7225 (OUTLIER) cc_final: 0.6958 (mtt-85) REVERT: R 200 MET cc_start: 0.7192 (mtt) cc_final: 0.6764 (mmm) REVERT: R 242 THR cc_start: 0.7832 (t) cc_final: 0.7547 (m) REVERT: S 27 PHE cc_start: 0.8254 (OUTLIER) cc_final: 0.7845 (p90) REVERT: S 155 HIS cc_start: 0.8168 (t-90) cc_final: 0.7937 (t-90) outliers start: 53 outliers final: 27 residues processed: 217 average time/residue: 0.2455 time to fit residues: 70.7132 Evaluate side-chains 217 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.960 ------------------------------------------------------------------------------- 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 207 GLU 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 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 187 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain G residue 22 GLU 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 196 THR Chi-restraints excluded: chain R residue 205 LYS 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 27 PHE 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: 5.9990 chunk 94 optimal weight: 1.9990 chunk 110 optimal weight: 2.9990 chunk 108 optimal weight: 0.2980 chunk 100 optimal weight: 3.9990 chunk 39 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.155859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.126153 restraints weight = 13063.621| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.57 r_work: 0.3521 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9110 Z= 0.149 Angle : 0.577 9.263 12343 Z= 0.302 Chirality : 0.041 0.205 1408 Planarity : 0.004 0.051 1543 Dihedral : 4.950 60.059 1238 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 4.69 % Allowed : 25.31 % Favored : 70.00 % 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: 0.86 (0.25), residues: 1111 helix: 2.47 (0.25), residues: 410 sheet: 0.42 (0.29), residues: 276 loop : -1.29 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.004 0.001 HIS A 188 PHE 0.020 0.002 PHE B 199 TYR 0.017 0.002 TYR R 266 ARG 0.003 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.05307 ( 447) hydrogen bonds : angle 4.27080 ( 1296) SS BOND : bond 0.00589 ( 3) SS BOND : angle 1.01110 ( 6) covalent geometry : bond 0.00334 ( 9107) covalent geometry : angle 0.57720 (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 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 183 time to evaluate : 0.929 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6097 (OUTLIER) cc_final: 0.5803 (mt-10) REVERT: A 28 GLU cc_start: 0.7196 (OUTLIER) cc_final: 0.6855 (tt0) REVERT: A 51 LYS cc_start: 0.7875 (pttt) cc_final: 0.7660 (pttt) REVERT: B 217 MET cc_start: 0.8005 (OUTLIER) cc_final: 0.7371 (pmm) REVERT: B 258 ASP cc_start: 0.6292 (m-30) cc_final: 0.5985 (m-30) REVERT: B 259 GLN cc_start: 0.8107 (pm20) cc_final: 0.7905 (pm20) REVERT: G 22 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.7127 (mp0) REVERT: R 43 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5937 (pmm) REVERT: R 67 ASN cc_start: 0.6885 (m110) cc_final: 0.6589 (m110) REVERT: R 121 ARG cc_start: 0.7210 (OUTLIER) cc_final: 0.6929 (mtt-85) REVERT: R 200 MET cc_start: 0.7199 (mtt) cc_final: 0.6730 (mmm) REVERT: R 242 THR cc_start: 0.7877 (t) cc_final: 0.7664 (t) REVERT: S 27 PHE cc_start: 0.8274 (OUTLIER) cc_final: 0.7862 (p90) REVERT: S 155 HIS cc_start: 0.8169 (t-90) cc_final: 0.7908 (t-90) outliers start: 46 outliers final: 31 residues processed: 207 average time/residue: 0.2431 time to fit residues: 67.0060 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 185 time to evaluate : 0.957 ------------------------------------------------------------------------------- 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 A residue 348 LEU 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 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 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 251 LEU 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 143 VAL Chi-restraints excluded: chain S residue 210 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 90 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 64 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.4011 r_free = 0.4011 target = 0.153711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.124027 restraints weight = 13168.878| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 2.59 r_work: 0.3488 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7164 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 9110 Z= 0.215 Angle : 0.636 9.872 12343 Z= 0.335 Chirality : 0.043 0.219 1408 Planarity : 0.004 0.051 1543 Dihedral : 5.169 62.101 1238 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 5.82 % Allowed : 24.69 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.25), residues: 1111 helix: 2.23 (0.25), residues: 408 sheet: 0.29 (0.29), residues: 278 loop : -1.36 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP R 261 HIS 0.005 0.001 HIS A 188 PHE 0.026 0.002 PHE B 199 TYR 0.021 0.002 TYR S 223 ARG 0.004 0.000 ARG S 38 Details of bonding type rmsd hydrogen bonds : bond 0.06206 ( 447) hydrogen bonds : angle 4.48430 ( 1296) SS BOND : bond 0.00710 ( 3) SS BOND : angle 1.49407 ( 6) covalent geometry : bond 0.00497 ( 9107) covalent geometry : angle 0.63548 (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 248 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 191 time to evaluate : 1.011 Fit side-chains revert: symmetry clash REVERT: A 28 GLU cc_start: 0.7324 (OUTLIER) cc_final: 0.6894 (tt0) REVERT: A 318 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6518 (mm-30) REVERT: B 163 ASP cc_start: 0.6882 (t0) cc_final: 0.6648 (t0) REVERT: B 217 MET cc_start: 0.7965 (OUTLIER) cc_final: 0.7305 (pmm) REVERT: B 258 ASP cc_start: 0.6382 (m-30) cc_final: 0.6060 (m-30) REVERT: B 259 GLN cc_start: 0.8019 (pm20) cc_final: 0.7784 (pm20) REVERT: G 22 GLU cc_start: 0.7430 (OUTLIER) cc_final: 0.7131 (mp0) REVERT: R 43 MET cc_start: 0.6411 (OUTLIER) cc_final: 0.6063 (pmm) REVERT: R 67 ASN cc_start: 0.6912 (m110) cc_final: 0.6542 (m110) REVERT: R 121 ARG cc_start: 0.7117 (OUTLIER) cc_final: 0.6853 (mtt-85) REVERT: R 187 ILE cc_start: 0.8004 (mm) cc_final: 0.7783 (mt) REVERT: R 200 MET cc_start: 0.7246 (mtt) cc_final: 0.6757 (mmm) REVERT: R 242 THR cc_start: 0.7817 (t) cc_final: 0.7548 (m) REVERT: S 27 PHE cc_start: 0.8222 (OUTLIER) cc_final: 0.7807 (p90) REVERT: S 155 HIS cc_start: 0.8236 (t-90) cc_final: 0.7954 (t-90) REVERT: S 232 LYS cc_start: 0.7826 (OUTLIER) cc_final: 0.7336 (tmtt) outliers start: 57 outliers final: 37 residues processed: 219 average time/residue: 0.2378 time to fit residues: 70.0529 Evaluate side-chains 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 191 time to evaluate : 0.898 ------------------------------------------------------------------------------- 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 233 VAL Chi-restraints excluded: chain A residue 270 LYS Chi-restraints excluded: chain A residue 314 LYS Chi-restraints excluded: chain A residue 318 GLU 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 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 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 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 116 THR 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: 0.2980 chunk 8 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 96 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 47 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 0.0370 chunk 21 optimal weight: 0.5980 overall best weight: 0.4258 ------------------------------------------------------------------------------- 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 = 0.4046 r_free = 0.4046 target = 0.156892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126959 restraints weight = 13217.606| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.59 r_work: 0.3525 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7120 moved from start: 0.1634 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= 0.122 Angle : 0.581 10.955 12343 Z= 0.301 Chirality : 0.040 0.187 1408 Planarity : 0.004 0.051 1543 Dihedral : 4.941 60.262 1238 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.49 % Allowed : 26.43 % 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: 0.95 (0.26), residues: 1111 helix: 2.64 (0.25), residues: 407 sheet: 0.40 (0.30), residues: 276 loop : -1.26 (0.29), residues: 428 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 0.015 0.001 PHE B 199 TYR 0.019 0.001 TYR R 266 ARG 0.002 0.000 ARG B 256 Details of bonding type rmsd hydrogen bonds : bond 0.04814 ( 447) hydrogen bonds : angle 4.18474 ( 1296) SS BOND : bond 0.00541 ( 3) SS BOND : angle 1.09931 ( 6) covalent geometry : bond 0.00265 ( 9107) covalent geometry : angle 0.58056 (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 236 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 192 time to evaluate : 0.885 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.5918 (OUTLIER) cc_final: 0.5652 (mt-10) REVERT: A 10 LYS cc_start: 0.7315 (mtmm) cc_final: 0.7038 (mtmm) REVERT: A 24 ARG cc_start: 0.7545 (mtp-110) cc_final: 0.7303 (mtp-110) REVERT: B 125 ASN cc_start: 0.8249 (t0) cc_final: 0.7979 (t0) REVERT: B 217 MET cc_start: 0.7955 (OUTLIER) cc_final: 0.7300 (pmm) REVERT: B 258 ASP cc_start: 0.6327 (m-30) cc_final: 0.6026 (m-30) REVERT: B 259 GLN cc_start: 0.8122 (pm20) cc_final: 0.7883 (pm20) REVERT: G 22 GLU cc_start: 0.7390 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: R 43 MET cc_start: 0.6250 (OUTLIER) cc_final: 0.5908 (pmm) REVERT: R 121 ARG cc_start: 0.7178 (OUTLIER) cc_final: 0.6899 (mtt-85) REVERT: R 135 MET cc_start: 0.7083 (OUTLIER) cc_final: 0.6777 (ttm) REVERT: R 200 MET cc_start: 0.7205 (mtt) cc_final: 0.6717 (mmm) REVERT: R 242 THR cc_start: 0.7864 (t) cc_final: 0.7585 (m) REVERT: S 155 HIS cc_start: 0.8189 (t-90) cc_final: 0.7963 (t-90) REVERT: S 232 LYS cc_start: 0.7694 (OUTLIER) cc_final: 0.7366 (tmtt) outliers start: 44 outliers final: 29 residues processed: 215 average time/residue: 0.2369 time to fit residues: 67.6092 Evaluate side-chains 223 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.940 ------------------------------------------------------------------------------- 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 48 THR 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 B residue 61 MET 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 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 13 ARG Chi-restraints excluded: chain G residue 22 GLU 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 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 7 SER 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: 0.0040 chunk 71 optimal weight: 0.6980 chunk 60 optimal weight: 0.0770 chunk 90 optimal weight: 4.9990 chunk 100 optimal weight: 4.9990 chunk 39 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.4750 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 155 ASN B 295 ASN ** 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 = 0.4051 r_free = 0.4051 target = 0.157191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.127138 restraints weight = 13377.697| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 2.62 r_work: 0.3535 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9110 Z= 0.124 Angle : 0.577 8.780 12343 Z= 0.299 Chirality : 0.041 0.284 1408 Planarity : 0.004 0.052 1543 Dihedral : 4.881 60.310 1238 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 4.39 % Allowed : 26.33 % 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: 1.00 (0.26), residues: 1111 helix: 2.72 (0.25), residues: 407 sheet: 0.42 (0.30), residues: 272 loop : -1.24 (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 0.016 0.001 PHE B 199 TYR 0.018 0.001 TYR R 266 ARG 0.002 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04617 ( 447) hydrogen bonds : angle 4.14003 ( 1296) SS BOND : bond 0.00539 ( 3) SS BOND : angle 1.07984 ( 6) covalent geometry : bond 0.00273 ( 9107) covalent geometry : angle 0.57661 (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 234 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 191 time to evaluate : 0.975 Fit side-chains revert: symmetry clash REVERT: A 10 LYS cc_start: 0.7324 (mtmm) cc_final: 0.7053 (mtmm) REVERT: A 24 ARG cc_start: 0.7582 (mtp-110) cc_final: 0.7346 (mtp-110) REVERT: A 25 GLU cc_start: 0.7418 (tm-30) cc_final: 0.7074 (tm-30) REVERT: B 125 ASN cc_start: 0.8228 (t0) cc_final: 0.7998 (t0) REVERT: B 217 MET cc_start: 0.7960 (OUTLIER) cc_final: 0.7304 (pmm) REVERT: B 259 GLN cc_start: 0.8084 (pm20) cc_final: 0.7860 (pm20) REVERT: B 304 ARG cc_start: 0.7856 (ttm170) cc_final: 0.7636 (ttm170) REVERT: B 314 ARG cc_start: 0.7272 (mtt180) cc_final: 0.7062 (ttt180) REVERT: G 22 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.7116 (mp0) REVERT: R 43 MET cc_start: 0.6239 (OUTLIER) cc_final: 0.5908 (pmm) REVERT: R 105 ILE cc_start: 0.7344 (tt) cc_final: 0.7093 (mm) REVERT: R 121 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6898 (mtt-85) REVERT: R 135 MET cc_start: 0.7105 (OUTLIER) cc_final: 0.6811 (ttm) REVERT: R 200 MET cc_start: 0.7160 (mtt) cc_final: 0.6687 (mmm) REVERT: R 242 THR cc_start: 0.7862 (t) cc_final: 0.7572 (m) REVERT: S 143 VAL cc_start: 0.7678 (OUTLIER) cc_final: 0.7448 (m) REVERT: S 232 LYS cc_start: 0.7683 (OUTLIER) cc_final: 0.7428 (tmtt) outliers start: 43 outliers final: 31 residues processed: 212 average time/residue: 0.2403 time to fit residues: 67.9316 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 : 0.951 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET 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 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 228 ASP Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 281 SER Chi-restraints excluded: chain G residue 13 ARG 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 55 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 70 optimal weight: 0.5980 chunk 97 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 74 optimal weight: 0.7980 chunk 27 optimal weight: 0.6980 chunk 98 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 110 ASN B 155 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 = 0.4044 r_free = 0.4044 target = 0.156488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.126671 restraints weight = 13246.698| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 2.54 r_work: 0.3520 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1807 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= 0.152 Angle : 0.599 8.985 12343 Z= 0.313 Chirality : 0.041 0.270 1408 Planarity : 0.004 0.052 1543 Dihedral : 4.972 61.178 1238 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.39 % Allowed : 25.82 % Favored : 69.80 % 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: 0.93 (0.26), residues: 1111 helix: 2.60 (0.25), residues: 409 sheet: 0.39 (0.30), residues: 277 loop : -1.26 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 169 HIS 0.006 0.001 HIS S 155 PHE 0.020 0.001 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 0.05063 ( 447) hydrogen bonds : angle 4.22665 ( 1296) SS BOND : bond 0.00567 ( 3) SS BOND : angle 1.27468 ( 6) covalent geometry : bond 0.00344 ( 9107) covalent geometry : angle 0.59880 (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 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.950 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6125 (OUTLIER) cc_final: 0.5799 (mt-10) REVERT: A 10 LYS cc_start: 0.7430 (mtmm) cc_final: 0.7123 (mtmm) REVERT: A 25 GLU cc_start: 0.7451 (tm-30) cc_final: 0.7231 (tm-30) REVERT: A 28 GLU cc_start: 0.7156 (OUTLIER) cc_final: 0.6716 (tt0) REVERT: B 217 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7305 (pmm) REVERT: B 259 GLN cc_start: 0.8103 (pm20) cc_final: 0.7865 (pm20) REVERT: B 304 ARG cc_start: 0.7870 (ttm170) cc_final: 0.7609 (ttm170) REVERT: G 22 GLU cc_start: 0.7394 (OUTLIER) cc_final: 0.7121 (mp0) REVERT: R 43 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5884 (pmm) REVERT: R 121 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6944 (mtt-85) REVERT: R 200 MET cc_start: 0.7172 (mtt) cc_final: 0.6686 (mmm) REVERT: S 143 VAL cc_start: 0.7680 (OUTLIER) cc_final: 0.7273 (m) REVERT: S 232 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7439 (tmtt) outliers start: 43 outliers final: 35 residues processed: 204 average time/residue: 0.2460 time to fit residues: 66.6725 Evaluate side-chains 229 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 186 time to evaluate : 0.943 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET 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 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 13 ARG 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 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 7 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR 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 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 109 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 155 ASN B 239 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 = 0.4044 r_free = 0.4044 target = 0.156492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.126359 restraints weight = 13153.608| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.60 r_work: 0.3512 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3512 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 9110 Z= 0.155 Angle : 0.608 9.111 12343 Z= 0.318 Chirality : 0.041 0.266 1408 Planarity : 0.004 0.052 1543 Dihedral : 5.013 61.329 1238 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.59 % Favored : 95.41 % Rotamer: Outliers : 4.69 % Allowed : 25.82 % Favored : 69.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.26), residues: 1111 helix: 2.61 (0.25), residues: 409 sheet: 0.37 (0.30), residues: 277 loop : -1.31 (0.29), residues: 425 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 0.020 0.002 PHE B 199 TYR 0.015 0.002 TYR R 266 ARG 0.004 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.05133 ( 447) hydrogen bonds : angle 4.26025 ( 1296) SS BOND : bond 0.00600 ( 3) SS BOND : angle 1.23830 ( 6) covalent geometry : bond 0.00352 ( 9107) covalent geometry : angle 0.60726 (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 235 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 189 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 8 GLU cc_start: 0.6146 (OUTLIER) cc_final: 0.5833 (mt-10) REVERT: A 10 LYS cc_start: 0.7467 (mtmm) cc_final: 0.7167 (mtmm) REVERT: A 25 GLU cc_start: 0.7498 (tm-30) cc_final: 0.7293 (tm-30) REVERT: A 28 GLU cc_start: 0.7189 (OUTLIER) cc_final: 0.6712 (tt0) REVERT: A 216 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7377 (tm-30) REVERT: B 217 MET cc_start: 0.7956 (OUTLIER) cc_final: 0.7301 (pmm) REVERT: B 259 GLN cc_start: 0.8088 (pm20) cc_final: 0.7848 (pm20) REVERT: B 304 ARG cc_start: 0.7889 (ttm170) cc_final: 0.7634 (ttm170) REVERT: B 314 ARG cc_start: 0.7302 (mtt180) cc_final: 0.7092 (ttt180) REVERT: G 22 GLU cc_start: 0.7375 (OUTLIER) cc_final: 0.7101 (mp0) REVERT: R 43 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5902 (pmm) REVERT: R 121 ARG cc_start: 0.7256 (OUTLIER) cc_final: 0.6949 (mtt-85) REVERT: R 200 MET cc_start: 0.7180 (mtt) cc_final: 0.6695 (mmm) REVERT: S 143 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7289 (m) REVERT: S 232 LYS cc_start: 0.7749 (OUTLIER) cc_final: 0.7494 (tmtt) outliers start: 46 outliers final: 36 residues processed: 208 average time/residue: 0.2337 time to fit residues: 64.7805 Evaluate side-chains 233 residues out of total 980 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 189 time to evaluate : 0.968 ------------------------------------------------------------------------------- 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 207 GLU Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 247 MET 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 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 13 ARG 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 7 SER Chi-restraints excluded: chain S residue 25 SER Chi-restraints excluded: chain S residue 143 VAL Chi-restraints excluded: chain S residue 160 THR 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: 0.8980 chunk 78 optimal weight: 0.5980 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 76 optimal weight: 4.9990 chunk 85 optimal weight: 0.2980 chunk 11 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4051 r_free = 0.4051 target = 0.157025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.127366 restraints weight = 13212.449| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.52 r_work: 0.3534 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7122 moved from start: 0.1900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 9110 Z= 0.139 Angle : 0.594 9.026 12343 Z= 0.310 Chirality : 0.041 0.251 1408 Planarity : 0.004 0.052 1543 Dihedral : 4.988 60.847 1238 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 4.08 % Allowed : 26.73 % 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: 0.94 (0.26), residues: 1111 helix: 2.69 (0.25), residues: 407 sheet: 0.35 (0.30), residues: 277 loop : -1.31 (0.29), residues: 427 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 0.018 0.001 PHE B 199 TYR 0.016 0.002 TYR R 266 ARG 0.003 0.000 ARG B 68 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 447) hydrogen bonds : angle 4.21476 ( 1296) SS BOND : bond 0.00560 ( 3) SS BOND : angle 1.13854 ( 6) covalent geometry : bond 0.00314 ( 9107) covalent geometry : angle 0.59383 (12337) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4834.28 seconds wall clock time: 83 minutes 51.75 seconds (5031.75 seconds total)