Starting phenix.real_space_refine on Thu Jul 2 19:09:58 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695.map" model { file = "/net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dao_46695/07_2026/9dao_46695_neut.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 5 9.91 5 Mg 1 5.21 5 S 43 5.16 5 C 6171 2.51 5 N 1671 2.21 5 O 1913 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9804 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 3480 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 451, 3460 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 26, 'TRANS': 424} Conformer: "B" Number of residues, atoms: 451, 3460 Classifications: {'peptide': 451} Link IDs: {'PTRANS': 26, 'TRANS': 424} bond proxies already assigned to first conformer: 3533 Chain: "B" Number of atoms: 2914 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 372, 2910 Classifications: {'peptide': 372} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 353} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 372, 2910 Classifications: {'peptide': 372} Link IDs: {'PCIS': 3, 'PTRANS': 15, 'TRANS': 353} Chain breaks: 1 bond proxies already assigned to first conformer: 2957 Chain: "H" Number of atoms: 1738 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 227, 1721 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Conformer: "B" Number of residues, atoms: 227, 1721 Classifications: {'peptide': 227} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 212} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 bond proxies already assigned to first conformer: 1747 Chain: "L" Number of atoms: 1666 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 214, 1666 Classifications: {'peptide': 214} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 204} Chain breaks: 1 Chain: "A" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 0 Ad-hoc single atom residues: {' CA': 4} Chain breaks: 4 Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 1 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N AGLN A 177 " occ=0.56 ... (16 atoms not shown) pdb=" NE2BGLN A 177 " occ=0.44 residue: pdb=" N AARG A 276 " occ=0.43 ... (20 atoms not shown) pdb=" NH2BARG A 276 " occ=0.57 residue: pdb=" N AARG H 98 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG H 98 " occ=0.50 residue: pdb=" N CYS L 214 " occ=0.15 ... (5 atoms not shown) pdb=" OXT CYS L 214 " occ=0.15 Time building chain proxies: 3.19, per 1000 atoms: 0.33 Number of scatterers: 9804 At special positions: 0 Unit cell: (77.4, 123.84, 152.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 5 19.99 S 43 16.00 Mg 1 11.99 O 1913 8.00 N 1671 7.00 C 6171 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 56 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 130 " distance=2.05 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 167 " distance=2.03 Simple disulfide: pdb=" SG CYS B 177 " - pdb=" SG CYS B 184 " distance=2.04 Simple disulfide: pdb=" SG CYS B 232 " - pdb=" SG CYS B 273 " distance=2.03 Simple disulfide: pdb=" SG CYS B 374 " - pdb=" SG CYS B 386 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 152 " - pdb=" SG CYS H 207 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.57 Conformation dependent library (CDL) restraints added in 468.2 milliseconds 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2326 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 23 sheets defined 11.3% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.20 Creating SS restraints... Processing helix chain 'A' and resid 151 through 158 removed outlier: 3.600A pdb=" N TYR A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 192 Processing helix chain 'A' and resid 200 through 206 Processing helix chain 'A' and resid 227 through 231 Processing helix chain 'A' and resid 259 through 264 Processing helix chain 'B' and resid 127 through 134 Processing helix chain 'B' and resid 137 through 146 removed outlier: 3.923A pdb=" N MET B 142 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N ARG B 143 " --> pdb=" O ALA B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 209 removed outlier: 3.701A pdb=" N PHE B 203 " --> pdb=" O GLN B 199 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LYS B 209 " --> pdb=" O GLU B 205 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 232 Processing helix chain 'B' and resid 232 through 237 Processing helix chain 'B' and resid 258 through 264 removed outlier: 3.966A pdb=" N ARG B 261 " --> pdb=" O LEU B 258 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU B 262 " --> pdb=" O ASP B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 281 through 286 removed outlier: 3.967A pdb=" N SER B 284 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N THR B 285 " --> pdb=" O SER B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 303 Processing helix chain 'B' and resid 314 through 323 removed outlier: 3.523A pdb=" N TYR B 318 " --> pdb=" O VAL B 314 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N GLU B 323 " --> pdb=" O GLN B 319 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 349 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 12 removed outlier: 6.358A pdb=" N ASP A 434 " --> pdb=" O ALA A 424 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 424 " --> pdb=" O ASP A 434 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N SER A 420 " --> pdb=" O GLY A 438 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 23 through 27 Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 79 removed outlier: 3.546A pdb=" N GLU A 75 " --> pdb=" O THR A 86 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 96 through 100 removed outlier: 3.702A pdb=" N SER A 96 " --> pdb=" O CYS A 107 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 173 through 175 Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 242 removed outlier: 6.508A pdb=" N VAL A 267 " --> pdb=" O ARG A 279 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG A 279 " --> pdb=" O VAL A 267 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N ILE A 269 " --> pdb=" O LEU A 277 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 293 through 296 Processing sheet with id=AA8, first strand: chain 'A' and resid 314 through 315 Processing sheet with id=AA9, first strand: chain 'A' and resid 360 through 364 removed outlier: 5.983A pdb=" N ASP A 373 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLN A 405 " --> pdb=" O VAL A 391 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 394 through 395 Processing sheet with id=AB2, first strand: chain 'B' and resid 60 through 65 removed outlier: 6.352A pdb=" N ARG B 87 " --> pdb=" O LEU B 64 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 84 Processing sheet with id=AB4, first strand: chain 'B' and resid 190 through 197 removed outlier: 5.514A pdb=" N HIS B 192 " --> pdb=" O ALA B 155 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N ALA B 155 " --> pdb=" O HIS B 192 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LEU B 196 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ILE B 151 " --> pdb=" O LEU B 196 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP B 119 " --> pdb=" O THR B 249 " (cutoff:3.500A) removed outlier: 8.879A pdb=" N THR B 329 " --> pdb=" O ILE B 304 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N LEU B 306 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N GLY B 331 " --> pdb=" O LEU B 306 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N PHE B 308 " --> pdb=" O GLY B 331 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AB6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.346A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N MET H 34 " --> pdb=" O ARG H 50 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N ARG H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N SER H 40 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N SER H 44 " --> pdb=" O SER H 40 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.346A pdb=" N GLU H 10 " --> pdb=" O THR H 122 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.151A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.151A pdb=" N TYR H 187 " --> pdb=" O GLY H 156 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 163 through 166 Processing sheet with id=AC2, first strand: chain 'L' and resid 4 through 6 Processing sheet with id=AC3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.589A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'L' and resid 114 through 118 removed outlier: 3.535A pdb=" N VAL L 133 " --> pdb=" O PHE L 118 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 153 through 155 removed outlier: 4.782A pdb=" N TRP L 148 " --> pdb=" O ARG L 155 " (cutoff:3.500A) removed outlier: 6.150A pdb=" N HIS L 198 " --> pdb=" O SER L 203 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N SER L 203 " --> pdb=" O HIS L 198 " (cutoff:3.500A) 375 hydrogen bonds defined for protein. 982 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.17 Time building geometry restraints manager: 0.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.10: 1 1.10 - 1.30: 1634 1.30 - 1.50: 4371 1.50 - 1.70: 3962 1.70 - 1.89: 62 Bond restraints: 10030 Sorted by residual: bond pdb=" CG PRO A 5 " pdb=" CD PRO A 5 " ideal model delta sigma weight residual 1.503 0.908 0.595 3.40e-02 8.65e+02 3.07e+02 bond pdb=" CB PRO A 5 " pdb=" CG PRO A 5 " ideal model delta sigma weight residual 1.492 1.166 0.326 5.00e-02 4.00e+02 4.25e+01 bond pdb=" N PRO A 5 " pdb=" CA PRO A 5 " ideal model delta sigma weight residual 1.467 1.520 -0.053 1.17e-02 7.31e+03 2.06e+01 bond pdb=" N PRO A 5 " pdb=" CD PRO A 5 " ideal model delta sigma weight residual 1.473 1.416 0.057 1.40e-02 5.10e+03 1.63e+01 bond pdb=" CA PRO A 5 " pdb=" CB PRO A 5 " ideal model delta sigma weight residual 1.537 1.472 0.065 1.87e-02 2.86e+03 1.22e+01 ... (remaining 10025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 14.76: 13630 14.76 - 29.52: 3 29.52 - 44.28: 0 44.28 - 59.04: 0 59.04 - 73.79: 1 Bond angle restraints: 13634 Sorted by residual: angle pdb=" CB PRO A 5 " pdb=" CG PRO A 5 " pdb=" CD PRO A 5 " ideal model delta sigma weight residual 106.10 179.89 -73.79 3.20e+00 9.77e-02 5.32e+02 angle pdb=" N PRO A 5 " pdb=" CD PRO A 5 " pdb=" CG PRO A 5 " ideal model delta sigma weight residual 103.20 80.54 22.66 1.50e+00 4.44e-01 2.28e+02 angle pdb=" CA PRO A 5 " pdb=" CB PRO A 5 " pdb=" CG PRO A 5 " ideal model delta sigma weight residual 104.50 77.20 27.30 1.90e+00 2.77e-01 2.07e+02 angle pdb=" CA PRO A 5 " pdb=" N PRO A 5 " pdb=" CD PRO A 5 " ideal model delta sigma weight residual 112.00 100.68 11.32 1.40e+00 5.10e-01 6.53e+01 angle pdb=" C ASP A 4 " pdb=" N PRO A 5 " pdb=" CA PRO A 5 " ideal model delta sigma weight residual 120.47 112.23 8.24 1.07e+00 8.73e-01 5.94e+01 ... (remaining 13629 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5226 17.70 - 35.39: 583 35.39 - 53.09: 133 53.09 - 70.78: 40 70.78 - 88.48: 18 Dihedral angle restraints: 6000 sinusoidal: 2348 harmonic: 3652 Sorted by residual: dihedral pdb=" CA PHE H 158 " pdb=" C PHE H 158 " pdb=" N PRO H 159 " pdb=" CA PRO H 159 " ideal model delta harmonic sigma weight residual -180.00 -125.81 -54.19 0 5.00e+00 4.00e-02 1.17e+02 dihedral pdb=" CA GLU H 160 " pdb=" C GLU H 160 " pdb=" N PRO H 161 " pdb=" CA PRO H 161 " ideal model delta harmonic sigma weight residual 180.00 137.73 42.27 0 5.00e+00 4.00e-02 7.15e+01 dihedral pdb=" CB CYS A 107 " pdb=" SG CYS A 107 " pdb=" SG CYS A 130 " pdb=" CB CYS A 130 " ideal model delta sinusoidal sigma weight residual 93.00 17.90 75.10 1 1.00e+01 1.00e-02 7.13e+01 ... (remaining 5997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1074 0.042 - 0.085: 297 0.085 - 0.127: 114 0.127 - 0.170: 10 0.170 - 0.212: 2 Chirality restraints: 1497 Sorted by residual: chirality pdb=" CA PRO A 5 " pdb=" N PRO A 5 " pdb=" C PRO A 5 " pdb=" CB PRO A 5 " both_signs ideal model delta sigma weight residual False 2.72 2.93 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CA CYS A 130 " pdb=" N CYS A 130 " pdb=" C CYS A 130 " pdb=" CB CYS A 130 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.70e-01 chirality pdb=" CB VAL B 314 " pdb=" CA VAL B 314 " pdb=" CG1 VAL B 314 " pdb=" CG2 VAL B 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.48e-01 ... (remaining 1494 not shown) Planarity restraints: 1776 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP A 4 " 0.085 5.00e-02 4.00e+02 1.20e-01 2.30e+01 pdb=" N PRO A 5 " -0.206 5.00e-02 4.00e+02 pdb=" CA PRO A 5 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 5 " 0.074 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE H 158 " -0.066 5.00e-02 4.00e+02 1.01e-01 1.63e+01 pdb=" N PRO H 159 " 0.174 5.00e-02 4.00e+02 pdb=" CA PRO H 159 " -0.055 5.00e-02 4.00e+02 pdb=" CD PRO H 159 " -0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS H 211 " -0.042 5.00e-02 4.00e+02 6.41e-02 6.57e+00 pdb=" N PRO H 212 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 212 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 212 " -0.035 5.00e-02 4.00e+02 ... (remaining 1773 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.56: 81 2.56 - 3.15: 7123 3.15 - 3.73: 14099 3.73 - 4.32: 21425 4.32 - 4.90: 36571 Nonbonded interactions: 79299 Sorted by model distance: nonbonded pdb=" OG SER B 123 " pdb="MG MG B 801 " model vdw 1.978 2.170 nonbonded pdb=" OD1 ASP A 434 " pdb="CA CA A1104 " model vdw 2.179 3.250 nonbonded pdb=" NH1 ARG L 61 " pdb=" OD2 ASP L 82 " model vdw 2.183 3.120 nonbonded pdb=" OH TYR A 288 " pdb=" OD1 ASP B 259 " model vdw 2.185 3.040 nonbonded pdb=" OD1 ASP A 373 " pdb="CA CA A1103 " model vdw 2.210 3.250 ... (remaining 79294 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=0.00 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: 5.560 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: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.970 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:8.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 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 : 0.008 0.595 10040 Z= 0.248 Angle : 0.966 73.794 13654 Z= 0.446 Chirality : 0.045 0.212 1497 Planarity : 0.006 0.120 1776 Dihedral : 16.573 88.480 3644 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 2.59 % Allowed : 20.65 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.40 (0.24), residues: 1261 helix: -0.75 (0.48), residues: 116 sheet: 1.13 (0.24), residues: 489 loop : -1.33 (0.23), residues: 656 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 239 TYR 0.011 0.001 TYR A 448 PHE 0.020 0.002 PHE A 19 TRP 0.013 0.001 TRP A 113 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00756 / 0.25 (10030) covalent geometry : angle 0.96171 / 0.44 (13634) SS BOND : bond 0.00797 / 0.40 ( 10) SS BOND : angle 2.56259 / 1.12 ( 20) hydrogen bonds : bond 0.13057 / 8.43 ( 356) hydrogen bonds : angle 7.32529 / 4.99 ( 982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 87 time to evaluate : 0.228 Fit side-chains REVERT: A 275 GLN cc_start: 0.7265 (OUTLIER) cc_final: 0.6964 (mp10) REVERT: H 10 GLU cc_start: 0.8133 (OUTLIER) cc_final: 0.7135 (mm-30) outliers start: 24 outliers final: 20 residues processed: 108 average time/residue: 0.6706 time to fit residues: 77.3203 Evaluate side-chains 107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 SER Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 220 SER Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 131 ILE Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 277 SER Chi-restraints excluded: chain H residue 10 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain H residue 216 THR Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 61 ARG Chi-restraints excluded: chain L residue 77 SER Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 108 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 0.0060 chunk 123 optimal weight: 5.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 111 GLN A 215 HIS A 405 GLN B 342 GLN H 52 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.199218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.151456 restraints weight = 25125.340| |-----------------------------------------------------------------------------| r_work (start): 0.3680 rms_B_bonded: 5.23 r_work: 0.3280 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3244 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3244 r_free = 0.3244 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3243 r_free = 0.3243 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (8 function evaluations) r_final: 0.3243 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.0675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 10040 Z= 0.188 Angle : 0.724 16.710 13654 Z= 0.370 Chirality : 0.048 0.171 1497 Planarity : 0.006 0.102 1776 Dihedral : 7.036 71.197 1428 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 3.70 % Allowed : 18.61 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.50 (0.24), residues: 1261 helix: -0.57 (0.47), residues: 116 sheet: 0.91 (0.24), residues: 515 loop : -1.40 (0.23), residues: 630 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 108 TYR 0.013 0.002 TYR H 110 PHE 0.030 0.002 PHE A 19 TRP 0.014 0.002 TRP B 238 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00462 / 0.19 (10030) covalent geometry : angle 0.71701 / 0.37 (13634) SS BOND : bond 0.00932 / 0.46 ( 10) SS BOND : angle 2.73738 / 1.24 ( 20) hydrogen bonds : bond 0.03885 / 2.46 ( 356) hydrogen bonds : angle 6.01716 / 4.17 ( 982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.376 Fit side-chains REVERT: A 275 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: B 323 GLU cc_start: 0.8469 (OUTLIER) cc_final: 0.6915 (mp0) REVERT: B 391 ILE cc_start: 0.5558 (mt) cc_final: 0.5248 (mp) REVERT: H 5 ARG cc_start: 0.7315 (ttp-170) cc_final: 0.7095 (mtm110) REVERT: L 60 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.7451 (mptt) outliers start: 36 outliers final: 14 residues processed: 121 average time/residue: 0.6233 time to fit residues: 80.7205 Evaluate side-chains 102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 85 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 140 THR Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 113 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 76 optimal weight: 9.9990 chunk 43 optimal weight: 0.6980 chunk 105 optimal weight: 4.9990 chunk 17 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 215 HIS A 333 GLN A 405 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.199578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.154073 restraints weight = 26258.149| |-----------------------------------------------------------------------------| r_work (start): 0.3524 rms_B_bonded: 7.72 r_work: 0.3073 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3060 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3060 r_free = 0.3060 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3060 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10040 Z= 0.133 Angle : 0.617 15.496 13654 Z= 0.316 Chirality : 0.045 0.160 1497 Planarity : 0.005 0.100 1776 Dihedral : 5.957 69.418 1402 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 3.43 % Allowed : 19.44 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1261 helix: -0.28 (0.48), residues: 117 sheet: 0.94 (0.24), residues: 507 loop : -1.35 (0.23), residues: 637 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 108 TYR 0.012 0.001 TYR B 318 PHE 0.020 0.002 PHE A 19 TRP 0.013 0.001 TRP A 113 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.13 (10030) covalent geometry : angle 0.61029 / 0.31 (13634) SS BOND : bond 0.00851 / 0.42 ( 10) SS BOND : angle 2.50902 / 1.14 ( 20) hydrogen bonds : bond 0.03241 / 2.05 ( 356) hydrogen bonds : angle 5.68579 / 3.93 ( 982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 0.395 Fit side-chains REVERT: A 121 GLU cc_start: 0.7767 (pt0) cc_final: 0.7518 (pt0) REVERT: A 275 GLN cc_start: 0.7418 (OUTLIER) cc_final: 0.6951 (mp10) REVERT: A 280 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8417 (mt) REVERT: A 288 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7746 (m-80) REVERT: B 323 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.6844 (mp0) REVERT: B 387 MET cc_start: 0.7291 (mmp) cc_final: 0.7054 (mtt) REVERT: H 5 ARG cc_start: 0.7251 (ttp-170) cc_final: 0.6925 (mtm110) REVERT: L 60 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7633 (mptt) outliers start: 32 outliers final: 14 residues processed: 112 average time/residue: 0.6285 time to fit residues: 75.0957 Evaluate side-chains 105 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 26 optimal weight: 2.9990 chunk 22 optimal weight: 0.4980 chunk 35 optimal weight: 0.3980 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.8980 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 0.5980 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 215 HIS A 405 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.200655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.153746 restraints weight = 28592.974| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 5.53 r_work: 0.3337 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3324 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3324 r_free = 0.3324 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.3324 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 10040 Z= 0.121 Angle : 0.597 16.005 13654 Z= 0.305 Chirality : 0.044 0.177 1497 Planarity : 0.005 0.100 1776 Dihedral : 5.807 67.872 1400 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 3.70 % Allowed : 19.17 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1261 helix: -0.08 (0.48), residues: 117 sheet: 0.93 (0.24), residues: 500 loop : -1.30 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 108 TYR 0.012 0.001 TYR B 348 PHE 0.018 0.001 PHE A 19 TRP 0.013 0.001 TRP A 113 HIS 0.003 0.001 HIS B 255 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (10030) covalent geometry : angle 0.59022 / 0.30 (13634) SS BOND : bond 0.00835 / 0.41 ( 10) SS BOND : angle 2.38922 / 1.08 ( 20) hydrogen bonds : bond 0.03019 / 1.92 ( 356) hydrogen bonds : angle 5.52758 / 3.82 ( 982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 86 time to evaluate : 0.363 Fit side-chains REVERT: A 121 GLU cc_start: 0.7694 (pt0) cc_final: 0.7471 (pt0) REVERT: A 140 ARG cc_start: 0.8170 (OUTLIER) cc_final: 0.7893 (mmt-90) REVERT: A 275 GLN cc_start: 0.7630 (OUTLIER) cc_final: 0.7052 (mp10) REVERT: A 280 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 288 TYR cc_start: 0.8560 (OUTLIER) cc_final: 0.7771 (m-80) REVERT: A 395 GLN cc_start: 0.8239 (OUTLIER) cc_final: 0.7156 (pp30) REVERT: B 348 TYR cc_start: 0.5452 (t80) cc_final: 0.4514 (t80) REVERT: L 60 LYS cc_start: 0.7954 (OUTLIER) cc_final: 0.7607 (mptt) REVERT: L 90 GLN cc_start: 0.7903 (OUTLIER) cc_final: 0.7666 (pt0) outliers start: 34 outliers final: 12 residues processed: 114 average time/residue: 0.6125 time to fit residues: 74.5789 Evaluate side-chains 104 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 85 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 38 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 80 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 0.0060 chunk 40 optimal weight: 0.0980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 overall best weight: 0.9800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 78 ASN A 158 ASN A 215 HIS A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.198137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.153637 restraints weight = 28940.605| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 5.78 r_work: 0.3270 rms_B_bonded: 5.17 restraints_weight: 2.0000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3237 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 10040 Z= 0.165 Angle : 0.660 16.613 13654 Z= 0.335 Chirality : 0.046 0.177 1497 Planarity : 0.005 0.100 1776 Dihedral : 6.004 66.691 1400 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 3.61 % Allowed : 19.91 % Favored : 76.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.24), residues: 1261 helix: -0.15 (0.48), residues: 117 sheet: 0.91 (0.24), residues: 500 loop : -1.32 (0.23), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.011 0.002 TYR B 318 PHE 0.026 0.002 PHE A 19 TRP 0.013 0.002 TRP B 238 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00405 / 0.16 (10030) covalent geometry : angle 0.65199 / 0.33 (13634) SS BOND : bond 0.00921 / 0.46 ( 10) SS BOND : angle 2.67932 / 1.22 ( 20) hydrogen bonds : bond 0.03451 / 2.18 ( 356) hydrogen bonds : angle 5.61086 / 3.88 ( 982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 89 time to evaluate : 0.231 Fit side-chains REVERT: A 121 GLU cc_start: 0.7940 (pt0) cc_final: 0.7718 (pt0) REVERT: A 140 ARG cc_start: 0.8246 (OUTLIER) cc_final: 0.7931 (mmt-90) REVERT: A 275 GLN cc_start: 0.7697 (OUTLIER) cc_final: 0.7180 (mp10) REVERT: A 280 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8505 (mt) REVERT: A 288 TYR cc_start: 0.8672 (OUTLIER) cc_final: 0.7963 (m-80) REVERT: A 395 GLN cc_start: 0.8319 (OUTLIER) cc_final: 0.7337 (pp30) REVERT: B 348 TYR cc_start: 0.5489 (t80) cc_final: 0.4708 (t80) REVERT: B 387 MET cc_start: 0.7385 (mmp) cc_final: 0.7031 (mtt) REVERT: L 21 LEU cc_start: 0.8263 (OUTLIER) cc_final: 0.7974 (mt) REVERT: L 60 LYS cc_start: 0.7933 (OUTLIER) cc_final: 0.7596 (mptt) outliers start: 33 outliers final: 16 residues processed: 117 average time/residue: 0.5316 time to fit residues: 66.5834 Evaluate side-chains 107 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 84 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain H residue 194 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 21 LEU Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 94 optimal weight: 6.9990 chunk 97 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 70 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.199161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.154260 restraints weight = 33750.001| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 7.25 r_work: 0.3059 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3087 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3087 r_free = 0.3087 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10040 Z= 0.135 Angle : 0.614 16.538 13654 Z= 0.313 Chirality : 0.045 0.196 1497 Planarity : 0.005 0.097 1776 Dihedral : 5.888 65.669 1400 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.24 % Favored : 95.68 % Rotamer: Outliers : 3.61 % Allowed : 20.28 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.36 (0.24), residues: 1261 helix: -0.03 (0.48), residues: 118 sheet: 0.93 (0.24), residues: 500 loop : -1.28 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 386 TYR 0.018 0.001 TYR B 110 PHE 0.021 0.002 PHE A 19 TRP 0.012 0.001 TRP A 113 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.13 (10030) covalent geometry : angle 0.60661 / 0.31 (13634) SS BOND : bond 0.00872 / 0.43 ( 10) SS BOND : angle 2.50466 / 1.13 ( 20) hydrogen bonds : bond 0.03114 / 1.98 ( 356) hydrogen bonds : angle 5.49800 / 3.79 ( 982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 85 time to evaluate : 0.246 Fit side-chains REVERT: A 121 GLU cc_start: 0.7831 (pt0) cc_final: 0.7581 (pt0) REVERT: A 140 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7821 (mmt-90) REVERT: A 275 GLN cc_start: 0.7513 (OUTLIER) cc_final: 0.6945 (mp10) REVERT: A 280 LEU cc_start: 0.8631 (OUTLIER) cc_final: 0.8383 (mt) REVERT: A 288 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: A 395 GLN cc_start: 0.8187 (OUTLIER) cc_final: 0.7106 (pp30) REVERT: B 348 TYR cc_start: 0.5216 (t80) cc_final: 0.4463 (t80) REVERT: B 387 MET cc_start: 0.7176 (mmp) cc_final: 0.6975 (mtt) REVERT: L 60 LYS cc_start: 0.7974 (OUTLIER) cc_final: 0.7598 (mptt) REVERT: L 90 GLN cc_start: 0.7838 (OUTLIER) cc_final: 0.7528 (pt0) outliers start: 33 outliers final: 16 residues processed: 112 average time/residue: 0.5655 time to fit residues: 67.7232 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 90 GLN Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 75 optimal weight: 0.6980 chunk 112 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 66 optimal weight: 0.0060 chunk 79 optimal weight: 20.0000 chunk 85 optimal weight: 2.9990 chunk 122 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 overall best weight: 1.1398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 215 HIS A 299 ASN B 82 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.197006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.151157 restraints weight = 22996.814| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 7.92 r_work: 0.3083 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3066 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3066 r_free = 0.3066 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3066 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.094 10040 Z= 0.182 Angle : 0.682 17.978 13654 Z= 0.346 Chirality : 0.047 0.207 1497 Planarity : 0.005 0.099 1776 Dihedral : 6.109 65.527 1400 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % Rotamer: Outliers : 3.70 % Allowed : 20.19 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.44 (0.23), residues: 1261 helix: -0.13 (0.47), residues: 116 sheet: 0.87 (0.23), residues: 510 loop : -1.34 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 352 TYR 0.019 0.002 TYR B 110 PHE 0.028 0.002 PHE A 19 TRP 0.015 0.002 TRP B 238 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.18 (10030) covalent geometry : angle 0.67403 / 0.34 (13634) SS BOND : bond 0.00979 / 0.49 ( 10) SS BOND : angle 2.84362 / 1.28 ( 20) hydrogen bonds : bond 0.03582 / 2.27 ( 356) hydrogen bonds : angle 5.60717 / 3.88 ( 982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 91 time to evaluate : 0.293 Fit side-chains REVERT: A 121 GLU cc_start: 0.7892 (pt0) cc_final: 0.7646 (pt0) REVERT: A 140 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7851 (mmt-90) REVERT: A 275 GLN cc_start: 0.7572 (OUTLIER) cc_final: 0.7007 (mp10) REVERT: A 280 LEU cc_start: 0.8674 (OUTLIER) cc_final: 0.8369 (mt) REVERT: A 288 TYR cc_start: 0.8591 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: A 395 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7219 (pp30) REVERT: B 143 ARG cc_start: 0.7762 (OUTLIER) cc_final: 0.7389 (mmt-90) REVERT: B 323 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7171 (mp0) REVERT: B 348 TYR cc_start: 0.5303 (t80) cc_final: 0.4473 (t80) REVERT: B 387 MET cc_start: 0.7155 (mmp) cc_final: 0.6901 (mtt) REVERT: L 60 LYS cc_start: 0.8092 (OUTLIER) cc_final: 0.7715 (mptt) REVERT: L 197 THR cc_start: 0.6801 (m) cc_final: 0.6520 (t) outliers start: 34 outliers final: 19 residues processed: 117 average time/residue: 0.5536 time to fit residues: 69.1903 Evaluate side-chains 119 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 92 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 206 GLU Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 60 LYS Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 86 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 7.9990 chunk 95 optimal weight: 9.9990 chunk 93 optimal weight: 0.7980 chunk 62 optimal weight: 2.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.196195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.154110 restraints weight = 23111.022| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 4.16 r_work: 0.3279 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3279 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3268 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3268 r_free = 0.3268 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (6 function evaluations) r_final: 0.3268 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8530 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.097 10040 Z= 0.193 Angle : 0.697 18.211 13654 Z= 0.354 Chirality : 0.048 0.207 1497 Planarity : 0.006 0.098 1776 Dihedral : 6.230 65.719 1400 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.04 % Favored : 94.80 % Rotamer: Outliers : 3.80 % Allowed : 20.37 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.53 (0.23), residues: 1261 helix: -0.28 (0.46), residues: 116 sheet: 0.82 (0.23), residues: 510 loop : -1.41 (0.23), residues: 635 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.017 0.002 TYR B 110 PHE 0.029 0.002 PHE A 19 TRP 0.016 0.002 TRP B 238 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.19 (10030) covalent geometry : angle 0.68877 / 0.35 (13634) SS BOND : bond 0.01016 / 0.51 ( 10) SS BOND : angle 2.91010 / 1.32 ( 20) hydrogen bonds : bond 0.03653 / 2.31 ( 356) hydrogen bonds : angle 5.65756 / 3.91 ( 982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 87 time to evaluate : 0.361 Fit side-chains REVERT: A 121 GLU cc_start: 0.7900 (pt0) cc_final: 0.7689 (pt0) REVERT: A 140 ARG cc_start: 0.8231 (OUTLIER) cc_final: 0.7911 (mmt-90) REVERT: A 275 GLN cc_start: 0.7735 (OUTLIER) cc_final: 0.7164 (mp10) REVERT: A 280 LEU cc_start: 0.8807 (OUTLIER) cc_final: 0.8444 (mt) REVERT: A 288 TYR cc_start: 0.8651 (OUTLIER) cc_final: 0.7937 (m-80) REVERT: A 395 GLN cc_start: 0.8312 (OUTLIER) cc_final: 0.7327 (pp30) REVERT: B 323 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7288 (mp0) REVERT: B 335 MET cc_start: 0.7932 (tpp) cc_final: 0.7673 (mmm) REVERT: B 348 TYR cc_start: 0.5479 (t80) cc_final: 0.4676 (t80) REVERT: B 389 LEU cc_start: 0.7196 (mt) cc_final: 0.6839 (tt) outliers start: 35 outliers final: 21 residues processed: 115 average time/residue: 0.5847 time to fit residues: 71.7064 Evaluate side-chains 114 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 87 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 0.0770 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.4980 chunk 105 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 112 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 0.8740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 7 GLN A 78 ASN A 215 HIS A 299 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.197548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.154993 restraints weight = 25029.880| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 5.10 r_work: 0.3236 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3257 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3257 r_free = 0.3257 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3257 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10040 Z= 0.153 Angle : 0.654 16.877 13654 Z= 0.332 Chirality : 0.046 0.186 1497 Planarity : 0.005 0.097 1776 Dihedral : 6.058 65.315 1400 Min Nonbonded Distance : 2.001 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.72 % Favored : 95.12 % Rotamer: Outliers : 3.15 % Allowed : 21.30 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.48 (0.23), residues: 1261 helix: -0.24 (0.47), residues: 118 sheet: 0.87 (0.24), residues: 502 loop : -1.36 (0.23), residues: 641 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.018 0.002 TYR B 110 PHE 0.024 0.002 PHE A 19 TRP 0.014 0.002 TRP A 235 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00375 / 0.15 (10030) covalent geometry : angle 0.64562 / 0.33 (13634) SS BOND : bond 0.00900 / 0.45 ( 10) SS BOND : angle 2.74475 / 1.23 ( 20) hydrogen bonds : bond 0.03308 / 2.10 ( 356) hydrogen bonds : angle 5.54186 / 3.83 ( 982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 85 time to evaluate : 0.304 Fit side-chains REVERT: A 121 GLU cc_start: 0.7955 (pt0) cc_final: 0.7744 (pt0) REVERT: A 140 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7910 (mmt-90) REVERT: A 275 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.7143 (mp10) REVERT: A 280 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8484 (mt) REVERT: A 288 TYR cc_start: 0.8653 (OUTLIER) cc_final: 0.7921 (m-80) REVERT: A 395 GLN cc_start: 0.8302 (OUTLIER) cc_final: 0.7339 (pp30) REVERT: B 143 ARG cc_start: 0.7798 (OUTLIER) cc_final: 0.7450 (mmt-90) REVERT: B 323 GLU cc_start: 0.8451 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: B 348 TYR cc_start: 0.5447 (t80) cc_final: 0.4765 (t80) REVERT: B 387 MET cc_start: 0.7326 (mmp) cc_final: 0.6927 (mtt) REVERT: B 389 LEU cc_start: 0.7214 (mt) cc_final: 0.6815 (tt) REVERT: H 13 LYS cc_start: 0.7966 (mppt) cc_final: 0.7522 (mmmt) outliers start: 28 outliers final: 19 residues processed: 110 average time/residue: 0.5721 time to fit residues: 67.0638 Evaluate side-chains 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 83 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain H residue 176 HIS Chi-restraints excluded: chain L residue 20 SER Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 45 optimal weight: 4.9990 chunk 55 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.198930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.158663 restraints weight = 23988.175| |-----------------------------------------------------------------------------| r_work (start): 0.3795 rms_B_bonded: 4.08 r_work: 0.3329 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.116 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.085 10040 Z= 0.129 Angle : 0.620 15.998 13654 Z= 0.315 Chirality : 0.045 0.175 1497 Planarity : 0.005 0.096 1776 Dihedral : 5.886 64.297 1400 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.40 % Favored : 95.44 % Rotamer: Outliers : 3.24 % Allowed : 20.83 % Favored : 75.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.38 (0.24), residues: 1261 helix: -0.05 (0.48), residues: 118 sheet: 0.91 (0.24), residues: 503 loop : -1.31 (0.23), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.017 0.001 TYR B 110 PHE 0.019 0.002 PHE A 19 TRP 0.013 0.001 TRP A 235 HIS 0.004 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.13 (10030) covalent geometry : angle 0.61181 / 0.31 (13634) SS BOND : bond 0.00835 / 0.40 ( 10) SS BOND : angle 2.62161 / 1.20 ( 20) hydrogen bonds : bond 0.03054 / 1.95 ( 356) hydrogen bonds : angle 5.43012 / 3.74 ( 982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2522 Ramachandran restraints generated. 1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 86 time to evaluate : 0.324 Fit side-chains REVERT: A 140 ARG cc_start: 0.8188 (OUTLIER) cc_final: 0.7909 (mmt-90) REVERT: A 275 GLN cc_start: 0.7781 (OUTLIER) cc_final: 0.7177 (mp10) REVERT: A 280 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8516 (mt) REVERT: A 288 TYR cc_start: 0.8613 (OUTLIER) cc_final: 0.7777 (m-80) REVERT: A 395 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7364 (pp30) REVERT: B 143 ARG cc_start: 0.7775 (OUTLIER) cc_final: 0.7406 (mmt-90) REVERT: B 323 GLU cc_start: 0.8465 (OUTLIER) cc_final: 0.7399 (mp0) REVERT: B 348 TYR cc_start: 0.5462 (t80) cc_final: 0.4847 (t80) REVERT: B 387 MET cc_start: 0.7349 (mmp) cc_final: 0.6947 (mtt) REVERT: B 389 LEU cc_start: 0.7249 (mt) cc_final: 0.6872 (tt) REVERT: H 13 LYS cc_start: 0.8000 (mppt) cc_final: 0.7565 (mmmt) outliers start: 29 outliers final: 18 residues processed: 108 average time/residue: 0.6172 time to fit residues: 71.1892 Evaluate side-chains 106 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 81 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 ARG Chi-restraints excluded: chain A residue 166 TYR Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN Chi-restraints excluded: chain A residue 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 396 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 401 SER Chi-restraints excluded: chain B residue 143 ARG Chi-restraints excluded: chain B residue 171 GLU Chi-restraints excluded: chain B residue 177 CYS Chi-restraints excluded: chain B residue 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 SER Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 323 GLU Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 122 THR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 0.5980 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 215 HIS A 299 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4191 r_free = 0.4191 target = 0.199178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.155245 restraints weight = 30486.603| |-----------------------------------------------------------------------------| r_work (start): 0.3717 rms_B_bonded: 6.02 r_work: 0.3269 rms_B_bonded: 5.03 restraints_weight: 2.0000 r_work (final): 0.3269 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3291 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3291 r_free = 0.3291 target_work(ls_wunit_k1) = 0.114 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3291 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.083 10040 Z= 0.127 Angle : 0.615 15.794 13654 Z= 0.313 Chirality : 0.045 0.173 1497 Planarity : 0.005 0.095 1776 Dihedral : 5.819 63.461 1400 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.16 % Favored : 95.68 % Rotamer: Outliers : 3.33 % Allowed : 20.46 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.96 % Cis-general : 0.00 % Twisted Proline : 2.99 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.35 (0.24), residues: 1261 helix: 0.05 (0.48), residues: 118 sheet: 0.94 (0.24), residues: 500 loop : -1.29 (0.23), residues: 643 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 352 TYR 0.017 0.001 TYR B 110 PHE 0.019 0.002 PHE A 19 TRP 0.013 0.001 TRP A 113 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (10030) covalent geometry : angle 0.60677 / 0.31 (13634) SS BOND : bond 0.00840 / 0.42 ( 10) SS BOND : angle 2.62041 / 1.22 ( 20) hydrogen bonds : bond 0.03021 / 1.92 ( 356) hydrogen bonds : angle 5.38862 / 3.71 ( 982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3442.40 seconds wall clock time: 59 minutes 23.74 seconds (3563.74 seconds total)