Starting phenix.real_space_refine on Tue Feb 11 11:14:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.map" model { file = "/net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gej_29972/02_2025/8gej_29972.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.020 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 9 5.16 5 C 3368 2.51 5 N 1029 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 5436 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 1718 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 247} Link IDs: {'PTRANS': 9, 'TRANS': 303} Chain breaks: 10 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 928 Unresolved non-hydrogen angles: 1174 Unresolved non-hydrogen dihedrals: 762 Unresolved non-hydrogen chiralities: 74 Planarities with less than four sites: {'GLN:plan1': 16, 'HIS:plan': 2, 'TYR:plan': 7, 'ASN:plan1': 16, 'TRP:plan': 4, 'ASP:plan': 20, 'PHE:plan': 11, 'GLU:plan': 25, 'ARG:plan': 23} Unresolved non-hydrogen planarities: 548 Chain: "B" Number of atoms: 1894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 323, 1894 Classifications: {'peptide': 323} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 191} Link IDs: {'PTRANS': 5, 'TRANS': 317} Chain breaks: 3 Unresolved non-hydrogen bonds: 601 Unresolved non-hydrogen angles: 757 Unresolved non-hydrogen dihedrals: 462 Unresolved non-hydrogen chiralities: 66 Planarities with less than four sites: {'GLN:plan1': 10, 'ASP:plan': 25, 'ASN:plan1': 14, 'TRP:plan': 1, 'HIS:plan': 2, 'ASN%COO:plan1': 1, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 18} Unresolved non-hydrogen planarities: 315 Chain: "G" Number of atoms: 232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 232 Classifications: {'peptide': 44} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PTRANS': 2, 'TRANS': 41} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 142 Unresolved non-hydrogen dihedrals: 97 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 3, 'PHE:plan': 1, 'GLU:plan': 5, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 62 Chain: "R" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 1577 Classifications: {'peptide': 270} Incomplete info: {'truncation_to_alanine': 180} Link IDs: {'PTRANS': 6, 'TRANS': 263} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 625 Unresolved non-hydrogen angles: 813 Unresolved non-hydrogen dihedrals: 506 Unresolved non-hydrogen chiralities: 91 Planarities with less than four sites: {'GLN:plan1': 8, 'HIS:plan': 1, 'TYR:plan': 7, 'ASN:plan1': 7, 'TRP:plan': 3, 'ASP:plan': 5, 'PHE:plan': 12, 'GLU:plan': 10, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 281 Chain: "R" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 15 Unusual residues: {'G1I': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.05, per 1000 atoms: 0.75 Number of scatterers: 5436 At special positions: 0 Unit cell: (66.78, 97.52, 127.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 9 16.00 O 1030 8.00 N 1029 7.00 C 3368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 184 " - pdb=" SG CYS R 190 " 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: 1.63 Conformation dependent library (CDL) restraints added in 983.3 milliseconds 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1816 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 12 sheets defined 50.6% alpha, 10.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 13 through 40 removed outlier: 3.933A pdb=" N GLN A 35 " --> pdb=" O GLN A 31 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N VAL A 36 " --> pdb=" O LYS A 32 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 91 through 113 Processing helix chain 'A' and resid 125 through 134 Processing helix chain 'A' and resid 145 through 156 Processing helix chain 'A' and resid 156 through 165 removed outlier: 3.571A pdb=" N ARG A 160 " --> pdb=" O ASP A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 185 Processing helix chain 'A' and resid 232 through 238 removed outlier: 3.708A pdb=" N GLN A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N PHE A 238 " --> pdb=" O TRP A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 278 Processing helix chain 'A' and resid 293 through 303 removed outlier: 3.521A pdb=" N ALA A 303 " --> pdb=" O GLU A 299 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 3.590A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 318 removed outlier: 4.407A pdb=" N ARG A 317 " --> pdb=" O PRO A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.815A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 388 removed outlier: 3.767A pdb=" N GLN A 384 " --> pdb=" O ARG A 380 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG A 385 " --> pdb=" O ASP A 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 8 through 26 removed outlier: 3.555A pdb=" N ALA B 26 " --> pdb=" O ARG B 22 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 37 removed outlier: 3.918A pdb=" N ILE B 33 " --> pdb=" O THR B 29 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE B 37 " --> pdb=" O ILE B 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 24 removed outlier: 3.913A pdb=" N ASN G 24 " --> pdb=" O LYS G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 45 Processing helix chain 'R' and resid 32 through 61 removed outlier: 3.928A pdb=" N ASN R 51 " --> pdb=" O ILE R 47 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N VAL R 54 " --> pdb=" O GLY R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 96 removed outlier: 3.910A pdb=" N VAL R 87 " --> pdb=" O GLY R 83 " (cutoff:3.500A) Proline residue: R 88 - end of helix Processing helix chain 'R' and resid 102 through 137 removed outlier: 3.718A pdb=" N PHE R 108 " --> pdb=" O PHE R 104 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ALA R 128 " --> pdb=" O LEU R 124 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 145 removed outlier: 4.211A pdb=" N GLN R 142 " --> pdb=" O PRO R 138 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER R 143 " --> pdb=" O PHE R 139 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 160 Processing helix chain 'R' and resid 165 through 172 removed outlier: 4.061A pdb=" N ILE R 169 " --> pdb=" O SER R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 181 through 187 removed outlier: 3.989A pdb=" N TYR R 185 " --> pdb=" O ALA R 181 " (cutoff:3.500A) Processing helix chain 'R' and resid 196 through 235 removed outlier: 3.559A pdb=" N ILE R 201 " --> pdb=" O GLN R 197 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA R 202 " --> pdb=" O ALA R 198 " (cutoff:3.500A) removed outlier: 5.683A pdb=" N VAL R 210 " --> pdb=" O VAL R 206 " (cutoff:3.500A) Proline residue: R 211 - end of helix Processing helix chain 'R' and resid 270 through 299 removed outlier: 3.763A pdb=" N ILE R 278 " --> pdb=" O THR R 274 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N PHE R 282 " --> pdb=" O ILE R 278 " (cutoff:3.500A) Proline residue: R 288 - end of helix Processing helix chain 'R' and resid 304 through 327 removed outlier: 3.933A pdb=" N GLY R 320 " --> pdb=" O TYR R 316 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N PHE R 321 " --> pdb=" O VAL R 317 " (cutoff:3.500A) Proline residue: R 323 - end of helix Processing helix chain 'R' and resid 332 through 339 removed outlier: 3.698A pdb=" N LEU R 339 " --> pdb=" O ALA R 335 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211 removed outlier: 5.930A pdb=" N HIS A 41 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 7.089A pdb=" N PHE A 222 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 5.947A pdb=" N LEU A 43 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARG A 42 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ILE A 245 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N LEU A 44 " --> pdb=" O ILE A 245 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 248 through 249 removed outlier: 6.237A pdb=" N VAL A 248 " --> pdb=" O ASN A 292 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 51 through 52 Processing sheet with id=AA4, first strand: chain 'B' and resid 62 through 63 removed outlier: 3.918A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 103 through 105 removed outlier: 3.506A pdb=" N CYS B 114 " --> pdb=" O SER B 122 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER B 122 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.531A pdb=" N VAL B 158 " --> pdb=" O ARG B 150 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 165 through 166 Processing sheet with id=AA8, first strand: chain 'B' and resid 169 through 170 removed outlier: 3.887A pdb=" N GLN B 175 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.849A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER B 201 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N LYS B 209 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 233 through 234 removed outlier: 6.660A pdb=" N LEU B 252 " --> pdb=" O LEU B 261 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.763A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TRP B 297 " --> pdb=" O LEU B 285 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 315 through 320 removed outlier: 6.909A pdb=" N GLY B 330 " --> pdb=" O SER B 316 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N LEU B 318 " --> pdb=" O ALA B 328 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA B 328 " --> pdb=" O LEU B 318 " (cutoff:3.500A) 362 hydrogen bonds defined for protein. 1062 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: 1.81 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 975 1.31 - 1.43: 1459 1.43 - 1.56: 3063 1.56 - 1.69: 1 1.69 - 1.81: 9 Bond restraints: 5507 Sorted by residual: bond pdb=" C SER R 319 " pdb=" O SER R 319 " ideal model delta sigma weight residual 1.237 1.182 0.055 1.17e-02 7.31e+03 2.22e+01 bond pdb=" CA LEU R 310 " pdb=" C LEU R 310 " ideal model delta sigma weight residual 1.524 1.479 0.046 1.28e-02 6.10e+03 1.28e+01 bond pdb=" CA ILE R 314 " pdb=" C ILE R 314 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.27e-02 6.20e+03 1.06e+01 bond pdb=" CA TYR R 316 " pdb=" C TYR R 316 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.03e+01 bond pdb=" CA TRP R 313 " pdb=" C TRP R 313 " ideal model delta sigma weight residual 1.523 1.483 0.040 1.34e-02 5.57e+03 9.00e+00 ... (remaining 5502 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 7466 1.40 - 2.79: 107 2.79 - 4.19: 29 4.19 - 5.58: 13 5.58 - 6.98: 2 Bond angle restraints: 7617 Sorted by residual: angle pdb=" N ASN R 322 " pdb=" CA ASN R 322 " pdb=" C ASN R 322 " ideal model delta sigma weight residual 113.16 106.18 6.98 1.42e+00 4.96e-01 2.41e+01 angle pdb=" C ILE R 314 " pdb=" N GLY R 315 " pdb=" CA GLY R 315 " ideal model delta sigma weight residual 119.94 114.54 5.40 1.11e+00 8.12e-01 2.36e+01 angle pdb=" C ILE R 314 " pdb=" CA ILE R 314 " pdb=" CB ILE R 314 " ideal model delta sigma weight residual 112.14 105.99 6.15 1.35e+00 5.49e-01 2.07e+01 angle pdb=" C ASN R 322 " pdb=" N PRO R 323 " pdb=" CA PRO R 323 " ideal model delta sigma weight residual 119.05 123.62 -4.57 1.11e+00 8.12e-01 1.69e+01 angle pdb=" N LEU R 324 " pdb=" CA LEU R 324 " pdb=" C LEU R 324 " ideal model delta sigma weight residual 111.28 107.39 3.89 1.09e+00 8.42e-01 1.27e+01 ... (remaining 7612 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.88: 2928 8.88 - 17.75: 115 17.75 - 26.62: 56 26.62 - 35.49: 19 35.49 - 44.37: 10 Dihedral angle restraints: 3128 sinusoidal: 366 harmonic: 2762 Sorted by residual: dihedral pdb=" CA SER B 74 " pdb=" C SER B 74 " pdb=" N GLN B 75 " pdb=" CA GLN B 75 " ideal model delta harmonic sigma weight residual 180.00 162.15 17.85 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA TRP B 169 " pdb=" C TRP B 169 " pdb=" N ASP B 170 " pdb=" CA ASP B 170 " ideal model delta harmonic sigma weight residual 180.00 164.51 15.49 0 5.00e+00 4.00e-02 9.60e+00 dihedral pdb=" CA HIS B 54 " pdb=" C HIS B 54 " pdb=" N LEU B 55 " pdb=" CA LEU B 55 " ideal model delta harmonic sigma weight residual -180.00 -165.58 -14.42 0 5.00e+00 4.00e-02 8.32e+00 ... (remaining 3125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 720 0.042 - 0.085: 187 0.085 - 0.127: 48 0.127 - 0.170: 1 0.170 - 0.212: 1 Chirality restraints: 957 Sorted by residual: chirality pdb=" CA TYR R 316 " pdb=" N TYR R 316 " pdb=" C TYR R 316 " pdb=" CB TYR R 316 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CAJ G1I R 501 " pdb=" CAF G1I R 501 " pdb=" CAI G1I R 501 " pdb=" OAM G1I R 501 " both_signs ideal model delta sigma weight residual False 2.40 2.54 -0.14 2.00e-01 2.50e+01 5.19e-01 chirality pdb=" CA ILE B 93 " pdb=" N ILE B 93 " pdb=" C ILE B 93 " pdb=" CB ILE B 93 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.75e-01 ... (remaining 954 not shown) Planarity restraints: 1037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE R 309 " 0.015 2.00e-02 2.50e+03 3.00e-02 9.03e+00 pdb=" C ILE R 309 " -0.052 2.00e-02 2.50e+03 pdb=" O ILE R 309 " 0.019 2.00e-02 2.50e+03 pdb=" N LEU R 310 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP R 313 " -0.009 2.00e-02 2.50e+03 1.83e-02 3.35e+00 pdb=" C TRP R 313 " 0.032 2.00e-02 2.50e+03 pdb=" O TRP R 313 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE R 314 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 310 " 0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C LEU R 310 " -0.028 2.00e-02 2.50e+03 pdb=" O LEU R 310 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU R 311 " 0.009 2.00e-02 2.50e+03 ... (remaining 1034 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 741 2.75 - 3.29: 5574 3.29 - 3.82: 8943 3.82 - 4.36: 8305 4.36 - 4.90: 14704 Nonbonded interactions: 38267 Sorted by model distance: nonbonded pdb=" OE1 GLN A 19 " pdb=" OG1 THR B 86 " model vdw 2.210 3.040 nonbonded pdb=" N SER B 147 " pdb=" O SER B 160 " model vdw 2.242 3.120 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.309 3.040 nonbonded pdb=" O ASP B 228 " pdb=" N ASP B 246 " model vdw 2.318 3.120 nonbonded pdb=" O ASN B 155 " pdb=" N ILE B 171 " model vdw 2.333 3.120 ... (remaining 38262 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 17.110 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 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 : 0.004 0.055 5507 Z= 0.250 Angle : 0.501 6.976 7617 Z= 0.327 Chirality : 0.040 0.212 957 Planarity : 0.003 0.036 1037 Dihedral : 8.378 44.368 1309 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.24 (0.29), residues: 906 helix: 2.79 (0.25), residues: 432 sheet: -0.03 (0.56), residues: 106 loop : -1.43 (0.30), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 297 HIS 0.003 0.001 HIS R 296 PHE 0.010 0.001 PHE A 340 TYR 0.011 0.001 TYR A 147 ARG 0.001 0.000 ARG R 131 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.595 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.1046 time to fit residues: 6.4178 Evaluate side-chains 30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 79 optimal weight: 8.9990 chunk 71 optimal weight: 0.8980 chunk 39 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 48 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 73 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 54 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.062819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.056308 restraints weight = 41577.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.057066 restraints weight = 28283.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.057605 restraints weight = 20828.453| |-----------------------------------------------------------------------------| r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.0871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5507 Z= 0.256 Angle : 0.449 5.537 7617 Z= 0.267 Chirality : 0.040 0.125 957 Planarity : 0.003 0.038 1037 Dihedral : 3.900 16.853 971 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.29), residues: 906 helix: 2.30 (0.25), residues: 442 sheet: -0.42 (0.54), residues: 114 loop : -1.69 (0.31), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 297 HIS 0.005 0.001 HIS R 296 PHE 0.016 0.001 PHE R 208 TYR 0.012 0.001 TYR A 147 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.583 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0718 time to fit residues: 4.7822 Evaluate side-chains 30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 35 optimal weight: 10.0000 chunk 78 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 93 optimal weight: 20.0000 chunk 89 optimal weight: 0.6980 chunk 24 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 66 optimal weight: 6.9990 chunk 3 optimal weight: 0.8980 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.062059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.055572 restraints weight = 41893.025| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056292 restraints weight = 28296.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056813 restraints weight = 20954.046| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5507 Z= 0.293 Angle : 0.472 5.436 7617 Z= 0.283 Chirality : 0.040 0.120 957 Planarity : 0.003 0.039 1037 Dihedral : 4.187 18.867 971 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.53 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.29), residues: 906 helix: 2.11 (0.25), residues: 438 sheet: -0.56 (0.53), residues: 114 loop : -1.84 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.005 0.001 HIS R 172 PHE 0.016 0.002 PHE B 292 TYR 0.014 0.001 TYR A 147 ARG 0.001 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.580 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0705 time to fit residues: 4.5753 Evaluate side-chains 30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 60 optimal weight: 9.9990 chunk 14 optimal weight: 0.2980 chunk 2 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 92 optimal weight: 9.9990 chunk 72 optimal weight: 8.9990 chunk 48 optimal weight: 0.0770 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 chunk 10 optimal weight: 30.0000 overall best weight: 2.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.062545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.056067 restraints weight = 42580.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3029 r_free = 0.3029 target = 0.056812 restraints weight = 28603.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.057353 restraints weight = 21047.993| |-----------------------------------------------------------------------------| r_work (final): 0.3043 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5507 Z= 0.213 Angle : 0.416 5.307 7617 Z= 0.246 Chirality : 0.040 0.120 957 Planarity : 0.003 0.043 1037 Dihedral : 3.910 18.260 971 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.29), residues: 906 helix: 2.24 (0.25), residues: 435 sheet: -0.50 (0.54), residues: 107 loop : -1.86 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.018 0.002 PHE R 208 TYR 0.011 0.001 TYR A 147 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.671 Fit side-chains REVERT: A 382 ILE cc_start: 0.9274 (mm) cc_final: 0.9019 (mm) outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0749 time to fit residues: 5.2632 Evaluate side-chains 32 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 3 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 86 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 10 optimal weight: 7.9990 chunk 84 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 55 optimal weight: 8.9990 chunk 46 optimal weight: 9.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.062145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.055680 restraints weight = 41760.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.056401 restraints weight = 28183.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.056936 restraints weight = 20901.853| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5507 Z= 0.251 Angle : 0.444 5.343 7617 Z= 0.265 Chirality : 0.040 0.121 957 Planarity : 0.003 0.042 1037 Dihedral : 4.020 19.226 971 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 3.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.29), residues: 906 helix: 2.15 (0.25), residues: 441 sheet: -0.49 (0.54), residues: 106 loop : -1.91 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.007 0.001 HIS R 296 PHE 0.016 0.001 PHE R 208 TYR 0.013 0.001 TYR A 147 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.565 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0717 time to fit residues: 4.7374 Evaluate side-chains 29 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 73 optimal weight: 2.9990 chunk 52 optimal weight: 0.0770 chunk 24 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 57 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 chunk 89 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.2144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.063616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.057146 restraints weight = 41317.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.057900 restraints weight = 27603.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.058455 restraints weight = 20200.388| |-----------------------------------------------------------------------------| r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5507 Z= 0.121 Angle : 0.371 5.222 7617 Z= 0.215 Chirality : 0.039 0.117 957 Planarity : 0.003 0.044 1037 Dihedral : 3.503 16.712 971 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.29), residues: 906 helix: 2.46 (0.25), residues: 442 sheet: -0.48 (0.54), residues: 101 loop : -1.76 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 63 HIS 0.002 0.001 HIS B 54 PHE 0.017 0.001 PHE R 208 TYR 0.010 0.001 TYR R 219 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.595 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0844 time to fit residues: 5.8336 Evaluate side-chains 30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 20.0000 chunk 60 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 chunk 82 optimal weight: 0.2980 chunk 35 optimal weight: 0.0060 chunk 6 optimal weight: 9.9990 chunk 77 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 0.8980 overall best weight: 0.6198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3247 r_free = 0.3247 target = 0.064909 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.058443 restraints weight = 41175.445| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059215 restraints weight = 27523.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.059775 restraints weight = 20089.050| |-----------------------------------------------------------------------------| r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.017 5507 Z= 0.085 Angle : 0.346 5.378 7617 Z= 0.196 Chirality : 0.039 0.118 957 Planarity : 0.002 0.044 1037 Dihedral : 2.983 15.087 971 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.29), residues: 906 helix: 2.75 (0.24), residues: 450 sheet: -0.75 (0.49), residues: 123 loop : -1.44 (0.33), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 169 HIS 0.002 0.000 HIS B 54 PHE 0.025 0.001 PHE R 208 TYR 0.011 0.001 TYR R 219 ARG 0.002 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.630 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 38 average time/residue: 0.0793 time to fit residues: 5.6549 Evaluate side-chains 32 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 32 time to evaluate : 0.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 40 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 17 optimal weight: 0.1980 chunk 42 optimal weight: 10.0000 chunk 60 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 43 optimal weight: 9.9990 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 87 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.064345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.057911 restraints weight = 41327.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.058678 restraints weight = 27528.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.059213 restraints weight = 20188.105| |-----------------------------------------------------------------------------| r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5507 Z= 0.114 Angle : 0.353 5.336 7617 Z= 0.202 Chirality : 0.039 0.121 957 Planarity : 0.002 0.043 1037 Dihedral : 3.032 14.538 971 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.30), residues: 906 helix: 2.92 (0.25), residues: 450 sheet: -0.63 (0.49), residues: 122 loop : -1.40 (0.33), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.001 PHE R 208 TYR 0.008 0.001 TYR R 219 ARG 0.001 0.000 ARG B 22 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.667 Fit side-chains REVERT: R 136 THR cc_start: 0.8137 (t) cc_final: 0.7822 (p) outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0772 time to fit residues: 5.2653 Evaluate side-chains 31 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 46 optimal weight: 9.9990 chunk 90 optimal weight: 3.9990 chunk 80 optimal weight: 0.1980 chunk 51 optimal weight: 9.9990 chunk 35 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.062348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055846 restraints weight = 41585.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.056587 restraints weight = 27907.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057095 restraints weight = 20650.483| |-----------------------------------------------------------------------------| r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5507 Z= 0.281 Angle : 0.450 5.339 7617 Z= 0.270 Chirality : 0.040 0.121 957 Planarity : 0.003 0.042 1037 Dihedral : 3.876 17.623 971 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.29), residues: 906 helix: 2.53 (0.25), residues: 440 sheet: -0.52 (0.53), residues: 102 loop : -1.58 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 297 HIS 0.004 0.001 HIS G 44 PHE 0.020 0.002 PHE R 208 TYR 0.013 0.001 TYR A 147 ARG 0.001 0.000 ARG R 221 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0766 time to fit residues: 5.1615 Evaluate side-chains 30 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 20.0000 chunk 54 optimal weight: 5.9990 chunk 10 optimal weight: 40.0000 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 89 optimal weight: 0.0980 chunk 13 optimal weight: 20.0000 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.061807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.055283 restraints weight = 41692.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.056027 restraints weight = 28056.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.056466 restraints weight = 20695.545| |-----------------------------------------------------------------------------| r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5507 Z= 0.325 Angle : 0.488 5.351 7617 Z= 0.294 Chirality : 0.041 0.118 957 Planarity : 0.003 0.040 1037 Dihedral : 4.309 20.035 971 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.32 (0.29), residues: 906 helix: 2.00 (0.25), residues: 441 sheet: -0.74 (0.54), residues: 101 loop : -1.84 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 297 HIS 0.005 0.001 HIS G 44 PHE 0.017 0.002 PHE A 340 TYR 0.015 0.002 TYR R 209 ARG 0.001 0.000 ARG R 131 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1812 Ramachandran restraints generated. 906 Oldfield, 0 Emsley, 906 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.641 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0768 time to fit residues: 5.1274 Evaluate side-chains 28 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 0 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 75 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 20.0000 chunk 35 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 26 optimal weight: 0.7980 chunk 92 optimal weight: 5.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.062649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.056141 restraints weight = 41996.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.056868 restraints weight = 28157.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.057420 restraints weight = 20823.757| |-----------------------------------------------------------------------------| r_work (final): 0.3049 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5507 Z= 0.190 Angle : 0.403 5.284 7617 Z= 0.237 Chirality : 0.040 0.119 957 Planarity : 0.003 0.041 1037 Dihedral : 3.821 18.557 971 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.29), residues: 906 helix: 2.25 (0.25), residues: 441 sheet: -0.70 (0.54), residues: 101 loop : -1.69 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 297 HIS 0.003 0.001 HIS A 357 PHE 0.026 0.002 PHE R 208 TYR 0.013 0.001 TYR A 360 ARG 0.002 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1430.73 seconds wall clock time: 26 minutes 15.81 seconds (1575.81 seconds total)