Starting phenix.real_space_refine on Wed Sep 17 16:49:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dao_46695/09_2025/9dao_46695_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dao_46695/09_2025/9dao_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_46695/09_2025/9dao_46695.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dao_46695/09_2025/9dao_46695.map" model { file = "/net/cci-nas-00/data/ceres_data/9dao_46695/09_2025/9dao_46695_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dao_46695/09_2025/9dao_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-2.0-5805/lib/python3.9/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, 4 Unusual residues: {' CA': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 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: 3.81, per 1000 atoms: 0.39 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: 0.91 Conformation dependent library (CDL) restraints added in 679.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.44 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: 1.76 Time building geometry restraints manager: 1.13 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 2.510 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 2.510 ... (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: 6.010 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 12.220 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 aren 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 covalent geometry : bond 0.00756 (10030) covalent geometry : angle 0.96171 (13634) SS BOND : bond 0.00797 ( 10) SS BOND : angle 2.56259 ( 20) hydrogen bonds : bond 0.13057 ( 356) hydrogen bonds : angle 7.32529 ( 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 : 0.329 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: 0.6923 time to fit residues: 79.4066 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 : 0.264 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4189 r_free = 0.4189 target = 0.199250 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.151481 restraints weight = 25078.028| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 5.12 r_work: 0.3270 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.0576 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= 0.185 Angle : 0.716 16.660 13654 Z= 0.366 Chirality : 0.047 0.168 1497 Planarity : 0.006 0.102 1776 Dihedral : 7.012 71.671 1428 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 3.70 % Allowed : 18.70 % Favored : 77.59 % 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 aren not related in a simple way. whole: -0.47 (0.24), residues: 1261 helix: -0.51 (0.48), residues: 115 sheet: 0.94 (0.24), residues: 509 loop : -1.37 (0.23), residues: 637 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 0.029 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 covalent geometry : bond 0.00458 (10030) covalent geometry : angle 0.70910 (13634) SS BOND : bond 0.00942 ( 10) SS BOND : angle 2.69578 ( 20) hydrogen bonds : bond 0.03916 ( 356) hydrogen bonds : angle 6.05180 ( 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 128 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 92 time to evaluate : 0.374 Fit side-chains REVERT: A 395 GLN cc_start: 0.8222 (OUTLIER) cc_final: 0.8014 (pm20) REVERT: B 323 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.6715 (mp0) REVERT: H 5 ARG cc_start: 0.7268 (ttp-170) cc_final: 0.7013 (mtm110) REVERT: L 60 LYS cc_start: 0.7854 (OUTLIER) cc_final: 0.7435 (mptt) outliers start: 36 outliers final: 12 residues processed: 120 average time/residue: 0.6210 time to fit residues: 79.2754 Evaluate side-chains 102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 87 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 348 THR Chi-restraints excluded: chain A residue 395 GLN Chi-restraints excluded: chain A residue 397 GLU 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: 0.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 43 optimal weight: 0.7980 chunk 105 optimal weight: 4.9990 chunk 17 optimal weight: 0.4980 chunk 42 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 15 optimal weight: 0.0980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4187 r_free = 0.4187 target = 0.199202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3779 r_free = 0.3779 target = 0.156388 restraints weight = 26466.442| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 4.73 r_work: 0.3070 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3070 ------------------------------------------------------------------------------- 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 | |-----------------------------------------------------------------------------| r_final: 0.3087 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.0749 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= 0.128 Angle : 0.612 15.519 13654 Z= 0.313 Chirality : 0.045 0.159 1497 Planarity : 0.005 0.100 1776 Dihedral : 5.346 52.519 1399 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 3.24 % Allowed : 19.54 % Favored : 77.22 % 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 aren not related in a simple way. whole: -0.39 (0.24), residues: 1261 helix: -0.28 (0.48), residues: 117 sheet: 0.92 (0.24), residues: 516 loop : -1.30 (0.23), residues: 628 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 0.019 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 covalent geometry : bond 0.00313 (10030) covalent geometry : angle 0.60501 (13634) SS BOND : bond 0.00829 ( 10) SS BOND : angle 2.48727 ( 20) hydrogen bonds : bond 0.03208 ( 356) hydrogen bonds : angle 5.69707 ( 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 118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 87 time to evaluate : 0.345 Fit side-chains REVERT: A 121 GLU cc_start: 0.7744 (pt0) cc_final: 0.7489 (pt0) REVERT: A 280 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8392 (mt) REVERT: A 288 TYR cc_start: 0.8531 (OUTLIER) cc_final: 0.7716 (m-80) REVERT: B 323 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.6774 (mp0) REVERT: B 387 MET cc_start: 0.7332 (mmp) cc_final: 0.7043 (mtt) REVERT: H 5 ARG cc_start: 0.7247 (ttp-170) cc_final: 0.6935 (mtm110) REVERT: L 60 LYS cc_start: 0.7959 (OUTLIER) cc_final: 0.7607 (mptt) outliers start: 31 outliers final: 12 residues processed: 112 average time/residue: 0.6649 time to fit residues: 79.3897 Evaluate side-chains 101 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 85 time to evaluate : 0.335 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR 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: 0.5980 chunk 35 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 0.9990 chunk 113 optimal weight: 1.9990 chunk 60 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 75 optimal weight: 8.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.4180 r_free = 0.4180 target = 0.197760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.150134 restraints weight = 28388.427| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 5.60 r_work: 0.3087 rms_B_bonded: 4.23 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3094 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3094 r_free = 0.3094 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 = 0.3094 r_free = 0.3094 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3094 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.0964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10040 Z= 0.159 Angle : 0.655 17.345 13654 Z= 0.333 Chirality : 0.046 0.195 1497 Planarity : 0.005 0.101 1776 Dihedral : 5.480 53.773 1397 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.24 % Favored : 95.60 % Rotamer: Outliers : 4.26 % Allowed : 18.80 % Favored : 76.94 % 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 aren not related in a simple way. whole: -0.45 (0.24), residues: 1261 helix: -0.28 (0.48), residues: 117 sheet: 0.91 (0.24), residues: 506 loop : -1.37 (0.23), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.012 0.002 TYR B 318 PHE 0.025 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 covalent geometry : bond 0.00390 (10030) covalent geometry : angle 0.64697 (13634) SS BOND : bond 0.00922 ( 10) SS BOND : angle 2.67770 ( 20) hydrogen bonds : bond 0.03449 ( 356) hydrogen bonds : angle 5.65770 ( 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 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 89 time to evaluate : 0.383 Fit side-chains REVERT: A 121 GLU cc_start: 0.7858 (pt0) cc_final: 0.7622 (pt0) REVERT: A 140 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7839 (mmt-90) REVERT: A 158 ASN cc_start: 0.6862 (m-40) cc_final: 0.6578 (m110) REVERT: A 280 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8394 (mt) REVERT: A 288 TYR cc_start: 0.8588 (OUTLIER) cc_final: 0.7859 (m-80) REVERT: B 348 TYR cc_start: 0.5388 (t80) cc_final: 0.4414 (t80) REVERT: H 5 ARG cc_start: 0.7264 (ttp-170) cc_final: 0.6960 (mtm110) REVERT: L 60 LYS cc_start: 0.7924 (OUTLIER) cc_final: 0.7615 (mptt) REVERT: L 90 GLN cc_start: 0.7831 (OUTLIER) cc_final: 0.7579 (pt0) REVERT: L 108 ARG cc_start: 0.8603 (ppt170) cc_final: 0.8133 (ptm160) outliers start: 40 outliers final: 17 residues processed: 122 average time/residue: 0.6067 time to fit residues: 79.1599 Evaluate side-chains 110 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 88 time to evaluate : 0.391 ------------------------------------------------------------------------------- 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 280 LEU Chi-restraints excluded: chain A residue 288 TYR Chi-restraints excluded: chain A residue 348 THR 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 211 SER Chi-restraints excluded: chain B residue 332 VAL Chi-restraints excluded: chain H residue 18 VAL 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 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 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: 2.9990 chunk 78 optimal weight: 4.9990 chunk 80 optimal weight: 8.9990 chunk 106 optimal weight: 4.9990 chunk 96 optimal weight: 9.9990 chunk 40 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS B 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.194508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.145792 restraints weight = 28926.508| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 7.00 r_work: 0.3043 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3131 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3131 r_free = 0.3131 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3131 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 10040 Z= 0.248 Angle : 0.762 18.777 13654 Z= 0.386 Chirality : 0.050 0.206 1497 Planarity : 0.006 0.100 1776 Dihedral : 5.893 58.342 1397 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.72 % Favored : 95.12 % Rotamer: Outliers : 4.44 % Allowed : 18.98 % Favored : 76.57 % 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 aren not related in a simple way. whole: -0.64 (0.23), residues: 1261 helix: -0.69 (0.45), residues: 122 sheet: 0.75 (0.23), residues: 512 loop : -1.41 (0.23), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 327 TYR 0.020 0.002 TYR B 110 PHE 0.035 0.003 PHE A 19 TRP 0.018 0.002 TRP B 238 HIS 0.005 0.002 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00617 (10030) covalent geometry : angle 0.75262 (13634) SS BOND : bond 0.01086 ( 10) SS BOND : angle 3.18763 ( 20) hydrogen bonds : bond 0.04130 ( 356) hydrogen bonds : angle 5.87120 ( 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 134 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 92 time to evaluate : 0.271 Fit side-chains REVERT: A 121 GLU cc_start: 0.7956 (pt0) cc_final: 0.7695 (pt0) REVERT: A 140 ARG cc_start: 0.8233 (OUTLIER) cc_final: 0.7717 (tpp-160) REVERT: A 243 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7417 (tm-30) REVERT: A 275 GLN cc_start: 0.7577 (OUTLIER) cc_final: 0.7039 (mp10) REVERT: A 395 GLN cc_start: 0.8112 (OUTLIER) cc_final: 0.6384 (pt0) REVERT: B 143 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7473 (mmt-90) REVERT: B 348 TYR cc_start: 0.5261 (t80) cc_final: 0.4340 (t80) REVERT: B 387 MET cc_start: 0.7242 (mmp) cc_final: 0.6964 (mtt) REVERT: H 5 ARG cc_start: 0.7303 (ttp-170) cc_final: 0.6976 (mtm110) REVERT: L 41 ASP cc_start: 0.7364 (t70) cc_final: 0.7057 (t70) REVERT: L 60 LYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7639 (mptt) outliers start: 42 outliers final: 20 residues processed: 124 average time/residue: 0.6723 time to fit residues: 89.0492 Evaluate side-chains 118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 92 time to evaluate : 0.325 ------------------------------------------------------------------------------- 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 243 GLU Chi-restraints excluded: chain A residue 270 LEU Chi-restraints excluded: chain A residue 275 GLN 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 182 THR Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 211 SER 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 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 90 GLN Chi-restraints excluded: chain L residue 133 VAL 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: 0.8980 chunk 40 optimal weight: 0.9980 chunk 91 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 16 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 70 optimal weight: 0.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 7 GLN A 215 HIS A 299 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.197306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.151284 restraints weight = 34316.436| |-----------------------------------------------------------------------------| r_work (start): 0.3481 rms_B_bonded: 7.11 r_work: 0.3035 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3034 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3034 r_free = 0.3034 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3034 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.1259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10040 Z= 0.148 Angle : 0.646 17.539 13654 Z= 0.329 Chirality : 0.046 0.203 1497 Planarity : 0.005 0.097 1776 Dihedral : 5.609 55.654 1397 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.56 % Favored : 95.28 % Rotamer: Outliers : 3.70 % Allowed : 19.72 % Favored : 76.57 % 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 aren not related in a simple way. whole: -0.54 (0.23), residues: 1261 helix: -0.27 (0.47), residues: 115 sheet: 0.82 (0.23), residues: 510 loop : -1.41 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG H 108 TYR 0.018 0.002 TYR B 110 PHE 0.023 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 covalent geometry : bond 0.00363 (10030) covalent geometry : angle 0.63808 (13634) SS BOND : bond 0.00956 ( 10) SS BOND : angle 2.75902 ( 20) hydrogen bonds : bond 0.03321 ( 356) hydrogen bonds : angle 5.63799 ( 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 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 95 time to evaluate : 0.267 Fit side-chains REVERT: A 121 GLU cc_start: 0.7924 (pt0) cc_final: 0.7691 (pt0) REVERT: A 140 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7854 (mmt-90) REVERT: A 158 ASN cc_start: 0.6897 (m-40) cc_final: 0.6613 (m110) REVERT: A 243 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 275 GLN cc_start: 0.7596 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 280 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8378 (mt) REVERT: A 395 GLN cc_start: 0.8080 (OUTLIER) cc_final: 0.6282 (pt0) REVERT: B 143 ARG cc_start: 0.7862 (OUTLIER) cc_final: 0.7520 (mmt-90) REVERT: B 348 TYR cc_start: 0.5457 (t80) cc_final: 0.4612 (t80) REVERT: B 387 MET cc_start: 0.7285 (mmp) cc_final: 0.7028 (mtt) REVERT: H 5 ARG cc_start: 0.7305 (ttp-170) cc_final: 0.6970 (mtm110) REVERT: L 197 THR cc_start: 0.7200 (m) cc_final: 0.6908 (t) outliers start: 34 outliers final: 18 residues processed: 120 average time/residue: 0.6672 time to fit residues: 85.2167 Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.393 ------------------------------------------------------------------------------- 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 243 GLU 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 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 211 SER Chi-restraints excluded: chain B residue 315 VAL 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 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: 2.9990 chunk 112 optimal weight: 0.8980 chunk 56 optimal weight: 0.7980 chunk 66 optimal weight: 0.3980 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 105 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 124 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.194054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.146662 restraints weight = 23913.349| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 5.50 r_work: 0.3211 rms_B_bonded: 4.26 restraints_weight: 0.5000 r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 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 = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.1483 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.102 10040 Z= 0.238 Angle : 0.762 19.646 13654 Z= 0.385 Chirality : 0.050 0.233 1497 Planarity : 0.006 0.105 1776 Dihedral : 5.944 58.124 1397 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.80 % Favored : 95.04 % Rotamer: Outliers : 3.89 % Allowed : 19.63 % 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 aren not related in a simple way. whole: -0.71 (0.23), residues: 1261 helix: -0.78 (0.45), residues: 122 sheet: 0.71 (0.23), residues: 514 loop : -1.46 (0.23), residues: 625 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 216 TYR 0.020 0.002 TYR B 110 PHE 0.034 0.003 PHE A 19 TRP 0.018 0.002 TRP B 238 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00591 (10030) covalent geometry : angle 0.75207 (13634) SS BOND : bond 0.01150 ( 10) SS BOND : angle 3.31050 ( 20) hydrogen bonds : bond 0.04090 ( 356) hydrogen bonds : angle 5.83902 ( 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 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 93 time to evaluate : 0.415 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7960 (pt0) cc_final: 0.7743 (pt0) REVERT: A 140 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7693 (tpp-160) REVERT: A 243 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.7477 (tm-30) REVERT: A 275 GLN cc_start: 0.7757 (OUTLIER) cc_final: 0.7163 (mp10) REVERT: A 280 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8453 (mt) REVERT: A 395 GLN cc_start: 0.8208 (OUTLIER) cc_final: 0.6514 (pt0) REVERT: B 143 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7590 (mmt-90) REVERT: B 187 MET cc_start: 0.8441 (ttt) cc_final: 0.8179 (ttt) REVERT: B 348 TYR cc_start: 0.5474 (t80) cc_final: 0.4623 (t80) REVERT: H 5 ARG cc_start: 0.7445 (ttp-170) cc_final: 0.7188 (mtm110) REVERT: L 197 THR cc_start: 0.7418 (m) cc_final: 0.7169 (t) outliers start: 36 outliers final: 19 residues processed: 121 average time/residue: 0.6407 time to fit residues: 82.6254 Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.245 ------------------------------------------------------------------------------- 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 243 GLU 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 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 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 133 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 122 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 86 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 95 optimal weight: 9.9990 chunk 93 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.195881 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.151148 restraints weight = 23210.141| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 4.30 r_work: 0.3251 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3238 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 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 = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.1492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 10040 Z= 0.175 Angle : 0.685 18.194 13654 Z= 0.347 Chirality : 0.047 0.208 1497 Planarity : 0.005 0.096 1776 Dihedral : 5.746 56.865 1397 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.64 % Favored : 95.20 % Rotamer: Outliers : 4.17 % Allowed : 19.81 % Favored : 76.02 % 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 aren not related in a simple way. whole: -0.65 (0.23), residues: 1261 helix: -0.48 (0.46), residues: 116 sheet: 0.78 (0.23), residues: 511 loop : -1.49 (0.23), residues: 634 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 216 TYR 0.018 0.002 TYR B 110 PHE 0.027 0.002 PHE A 19 TRP 0.014 0.002 TRP B 238 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00432 (10030) covalent geometry : angle 0.67602 (13634) SS BOND : bond 0.00983 ( 10) SS BOND : angle 2.97052 ( 20) hydrogen bonds : bond 0.03526 ( 356) hydrogen bonds : angle 5.68209 ( 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 129 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 90 time to evaluate : 0.384 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7912 (pt0) cc_final: 0.7690 (pt0) REVERT: A 140 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7895 (mmt-90) REVERT: A 243 GLU cc_start: 0.8410 (OUTLIER) cc_final: 0.7163 (tm-30) REVERT: A 275 GLN cc_start: 0.7763 (OUTLIER) cc_final: 0.7197 (mp10) REVERT: A 280 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8475 (mt) REVERT: A 395 GLN cc_start: 0.8190 (OUTLIER) cc_final: 0.6528 (pt0) REVERT: B 143 ARG cc_start: 0.7892 (OUTLIER) cc_final: 0.7540 (mmt-90) REVERT: B 348 TYR cc_start: 0.5595 (t80) cc_final: 0.4881 (t80) REVERT: B 387 MET cc_start: 0.7303 (mmp) cc_final: 0.6916 (mtt) REVERT: L 197 THR cc_start: 0.7378 (m) cc_final: 0.7172 (t) outliers start: 39 outliers final: 23 residues processed: 121 average time/residue: 0.6472 time to fit residues: 83.4957 Evaluate side-chains 118 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 89 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain A residue 243 GLU 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 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 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 12 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 133 VAL Chi-restraints excluded: chain L residue 175 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 114 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 118 optimal weight: 3.9990 chunk 112 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 122 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN A 215 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.194813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.149605 restraints weight = 24770.399| |-----------------------------------------------------------------------------| r_work (start): 0.3611 rms_B_bonded: 4.63 r_work: 0.3199 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 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 = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 10040 Z= 0.202 Angle : 0.723 18.892 13654 Z= 0.365 Chirality : 0.048 0.216 1497 Planarity : 0.006 0.100 1776 Dihedral : 5.847 57.486 1397 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.12 % Favored : 94.72 % 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 aren not related in a simple way. whole: -0.68 (0.23), residues: 1261 helix: -0.65 (0.45), residues: 122 sheet: 0.76 (0.23), residues: 511 loop : -1.50 (0.23), residues: 628 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 352 TYR 0.019 0.002 TYR B 110 PHE 0.030 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 covalent geometry : bond 0.00500 (10030) covalent geometry : angle 0.71362 (13634) SS BOND : bond 0.01070 ( 10) SS BOND : angle 3.12829 ( 20) hydrogen bonds : bond 0.03778 ( 356) hydrogen bonds : angle 5.74823 ( 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 123 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 89 time to evaluate : 0.372 Fit side-chains revert: symmetry clash REVERT: A 121 GLU cc_start: 0.7927 (pt0) cc_final: 0.7693 (pt0) REVERT: A 140 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7703 (tpp-160) REVERT: A 243 GLU cc_start: 0.8437 (OUTLIER) cc_final: 0.7287 (tm-30) REVERT: A 275 GLN cc_start: 0.7737 (OUTLIER) cc_final: 0.7149 (mp10) REVERT: A 280 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8450 (mt) REVERT: A 395 GLN cc_start: 0.8195 (OUTLIER) cc_final: 0.6567 (pt0) REVERT: B 143 ARG cc_start: 0.7871 (OUTLIER) cc_final: 0.7523 (mmt-90) REVERT: B 348 TYR cc_start: 0.5476 (t80) cc_final: 0.4704 (t80) REVERT: B 387 MET cc_start: 0.7235 (mmp) cc_final: 0.6922 (mtt) REVERT: H 13 LYS cc_start: 0.7986 (mppt) cc_final: 0.7541 (mmmt) outliers start: 34 outliers final: 23 residues processed: 116 average time/residue: 0.6271 time to fit residues: 77.6708 Evaluate side-chains 117 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 88 time to evaluate : 0.363 ------------------------------------------------------------------------------- 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 182 VAL Chi-restraints excluded: chain A residue 243 GLU 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 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 183 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 12 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 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 97 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 45 optimal weight: 0.3980 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 59 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.197860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.152037 restraints weight = 24221.982| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 5.36 r_work: 0.3280 rms_B_bonded: 4.19 restraints_weight: 0.5000 r_work (final): 0.3280 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3300 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3300 r_free = 0.3300 target_work(ls_wunit_k1) = 0.115 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3300 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.086 10040 Z= 0.125 Angle : 0.619 16.519 13654 Z= 0.315 Chirality : 0.045 0.183 1497 Planarity : 0.005 0.093 1776 Dihedral : 5.486 54.495 1397 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.32 % Favored : 95.52 % Rotamer: Outliers : 2.69 % Allowed : 21.39 % 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 aren not related in a simple way. whole: -0.49 (0.24), residues: 1261 helix: -0.22 (0.47), residues: 118 sheet: 0.87 (0.24), residues: 507 loop : -1.40 (0.23), residues: 636 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 352 TYR 0.018 0.001 TYR B 110 PHE 0.020 0.002 PHE L 91 TRP 0.014 0.001 TRP A 113 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00306 (10030) covalent geometry : angle 0.61162 (13634) SS BOND : bond 0.00857 ( 10) SS BOND : angle 2.54942 ( 20) hydrogen bonds : bond 0.03025 ( 356) hydrogen bonds : angle 5.50281 ( 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 109 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: A 140 ARG cc_start: 0.8153 (OUTLIER) cc_final: 0.7885 (mmt-90) REVERT: A 275 GLN cc_start: 0.7775 (OUTLIER) cc_final: 0.7172 (mp10) REVERT: A 280 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8506 (mt) REVERT: B 143 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7418 (mmt-90) REVERT: B 348 TYR cc_start: 0.5498 (t80) cc_final: 0.4899 (t80) REVERT: B 387 MET cc_start: 0.7204 (mmp) cc_final: 0.6906 (mtt) REVERT: H 13 LYS cc_start: 0.7984 (mppt) cc_final: 0.7551 (mmmt) outliers start: 23 outliers final: 16 residues processed: 105 average time/residue: 0.6836 time to fit residues: 76.3660 Evaluate side-chains 102 residues out of total 1071 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 82 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 182 VAL 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 348 THR 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 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 L residue 20 SER Chi-restraints excluded: chain L residue 133 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 125 random chunks: chunk 81 optimal weight: 3.9990 chunk 93 optimal weight: 2.9990 chunk 95 optimal weight: 20.0000 chunk 54 optimal weight: 0.9980 chunk 60 optimal weight: 0.9990 chunk 111 optimal weight: 1.9990 chunk 82 optimal weight: 0.9990 chunk 67 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 215 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.196504 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.148254 restraints weight = 31107.144| |-----------------------------------------------------------------------------| r_work (start): 0.3465 rms_B_bonded: 6.17 r_work: 0.3080 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.091 10040 Z= 0.161 Angle : 0.669 17.616 13654 Z= 0.339 Chirality : 0.046 0.199 1497 Planarity : 0.005 0.097 1776 Dihedral : 5.577 55.440 1397 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 4.48 % Favored : 95.36 % 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 aren not related in a simple way. whole: -0.48 (0.23), residues: 1261 helix: -0.20 (0.47), residues: 117 sheet: 0.91 (0.24), residues: 502 loop : -1.41 (0.23), residues: 642 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 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 113 HIS 0.005 0.001 HIS A 215 Details of bonding type rmsd covalent geometry : bond 0.00398 (10030) covalent geometry : angle 0.65983 (13634) SS BOND : bond 0.00965 ( 10) SS BOND : angle 2.93636 ( 20) hydrogen bonds : bond 0.03373 ( 356) hydrogen bonds : angle 5.56102 ( 982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3770.53 seconds wall clock time: 64 minutes 56.19 seconds (3896.19 seconds total)