Starting phenix.real_space_refine on Thu Nov 14 09:26:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_29972.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_29972.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_29972.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_29972.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gej_29972/11_2024/8gej_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-5513/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: 4.08, 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: 1.49 Conformation dependent library (CDL) restraints added in 1.0 seconds 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: 1.71 Time building geometry restraints manager: 1.66 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: 1.340 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: 17.300 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:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.670 ------------------------------------------------------------------------------- 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 : 0.558 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0846 time to fit residues: 5.6170 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 : 0.597 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 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 : 0.640 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0815 time to fit residues: 5.4638 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 : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 76 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 68 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 5507 Z= 0.149 Angle : 0.383 5.295 7617 Z= 0.222 Chirality : 0.039 0.119 957 Planarity : 0.002 0.039 1037 Dihedral : 3.485 15.657 971 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.29), residues: 906 helix: 2.56 (0.25), residues: 439 sheet: -0.42 (0.53), residues: 114 loop : -1.65 (0.30), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 63 HIS 0.002 0.001 HIS R 172 PHE 0.015 0.001 PHE R 208 TYR 0.008 0.001 TYR A 147 ARG 0.002 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 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.619 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0772 time to fit residues: 5.2941 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 : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 84 optimal weight: 0.0040 chunk 64 optimal weight: 3.9990 chunk 44 optimal weight: 9.9990 chunk 9 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 57 optimal weight: 8.9990 chunk 85 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 81 optimal weight: 0.0670 chunk 24 optimal weight: 5.9990 chunk 75 optimal weight: 0.9980 overall best weight: 1.1932 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.1368 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= 0.122 Angle : 0.366 5.274 7617 Z= 0.210 Chirality : 0.039 0.121 957 Planarity : 0.002 0.040 1037 Dihedral : 3.285 14.940 971 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % 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: 1.15 (0.29), residues: 906 helix: 2.66 (0.25), residues: 448 sheet: -0.35 (0.52), residues: 114 loop : -1.52 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 63 HIS 0.002 0.001 HIS B 54 PHE 0.018 0.001 PHE R 208 TYR 0.009 0.001 TYR R 219 ARG 0.001 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 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.600 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0742 time to fit residues: 5.1265 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 : 0.655 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 51 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 67 optimal weight: 8.9990 chunk 37 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 62 optimal weight: 9.9990 chunk 0 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 81 optimal weight: 0.6980 chunk 22 optimal weight: 7.9990 chunk 30 optimal weight: 0.8980 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.1327 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= 0.228 Angle : 0.425 5.299 7617 Z= 0.252 Chirality : 0.040 0.118 957 Planarity : 0.003 0.039 1037 Dihedral : 3.733 16.548 971 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.29), residues: 906 helix: 2.56 (0.25), residues: 436 sheet: -0.25 (0.53), residues: 105 loop : -1.64 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 297 HIS 0.003 0.001 HIS G 44 PHE 0.018 0.002 PHE R 208 TYR 0.012 0.001 TYR A 147 ARG 0.001 0.000 ARG A 342 *********************** 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 35 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.547 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 35 average time/residue: 0.0739 time to fit residues: 4.8965 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 : 0.575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 81 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 75 optimal weight: 0.7980 chunk 42 optimal weight: 9.9990 chunk 7 optimal weight: 20.0000 chunk 30 optimal weight: 5.9990 chunk 47 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5507 Z= 0.168 Angle : 0.387 5.230 7617 Z= 0.226 Chirality : 0.039 0.119 957 Planarity : 0.003 0.040 1037 Dihedral : 3.525 16.088 971 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.29), residues: 906 helix: 2.54 (0.25), residues: 442 sheet: -0.40 (0.52), residues: 106 loop : -1.73 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 297 HIS 0.002 0.001 HIS G 44 PHE 0.019 0.001 PHE R 208 TYR 0.010 0.001 TYR A 147 ARG 0.001 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 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.644 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0774 time to fit residues: 5.3680 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 : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 10 optimal weight: 20.0000 chunk 51 optimal weight: 9.9990 chunk 66 optimal weight: 10.0000 chunk 76 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 90 optimal weight: 0.3980 chunk 56 optimal weight: 9.9990 chunk 55 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 54 optimal weight: 3.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5507 Z= 0.213 Angle : 0.407 5.253 7617 Z= 0.240 Chirality : 0.040 0.118 957 Planarity : 0.003 0.040 1037 Dihedral : 3.664 16.853 971 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % 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: 0.83 (0.29), residues: 906 helix: 2.50 (0.25), residues: 441 sheet: -0.37 (0.53), residues: 105 loop : -1.78 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 PHE 0.020 0.001 PHE R 208 TYR 0.013 0.001 TYR A 360 ARG 0.001 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 36 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.692 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 36 average time/residue: 0.0775 time to fit residues: 5.4094 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 : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 27 optimal weight: 10.0000 chunk 17 optimal weight: 0.5980 chunk 57 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 20.0000 chunk 71 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 79 optimal weight: 2.9990 chunk 84 optimal weight: 0.0040 overall best weight: 1.2196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.1638 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 : 0.365 5.383 7617 Z= 0.211 Chirality : 0.039 0.114 957 Planarity : 0.002 0.041 1037 Dihedral : 3.299 15.187 971 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % 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: 1.19 (0.29), residues: 906 helix: 2.77 (0.25), residues: 443 sheet: -0.36 (0.52), residues: 108 loop : -1.53 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 63 HIS 0.002 0.001 HIS B 54 PHE 0.019 0.001 PHE R 193 TYR 0.010 0.001 TYR R 219 ARG 0.002 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 37 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.628 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 37 average time/residue: 0.0768 time to fit residues: 5.3667 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 : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 86 optimal weight: 9.9990 chunk 50 optimal weight: 9.9990 chunk 36 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 76 optimal weight: 2.9990 chunk 79 optimal weight: 10.0000 chunk 84 optimal weight: 0.9990 chunk 55 optimal weight: 9.9990 chunk 89 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5507 Z= 0.172 Angle : 0.387 5.246 7617 Z= 0.226 Chirality : 0.039 0.120 957 Planarity : 0.003 0.041 1037 Dihedral : 3.456 15.974 971 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: 1.11 (0.29), residues: 906 helix: 2.72 (0.25), residues: 443 sheet: -0.38 (0.53), residues: 101 loop : -1.58 (0.31), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.003 0.001 HIS B 54 PHE 0.010 0.001 PHE B 278 TYR 0.011 0.001 TYR A 360 ARG 0.001 0.000 ARG R 131 *********************** 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 34 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.663 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 34 average time/residue: 0.0752 time to fit residues: 5.1420 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 : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 42 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 93 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 74 optimal weight: 1.9990 chunk 7 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 79 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5507 Z= 0.356 Angle : 0.519 5.422 7617 Z= 0.317 Chirality : 0.041 0.135 957 Planarity : 0.003 0.039 1037 Dihedral : 4.411 19.789 971 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.29), residues: 906 helix: 1.96 (0.25), residues: 441 sheet: -0.68 (0.54), residues: 100 loop : -1.82 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 297 HIS 0.006 0.002 HIS R 296 PHE 0.024 0.002 PHE R 133 TYR 0.016 0.002 TYR A 360 ARG 0.001 0.000 ARG A 374 ********************** 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 33 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.618 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 33 average time/residue: 0.0735 time to fit residues: 4.9055 Evaluate side-chains 27 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 27 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 94 random chunks: chunk 68 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 74 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 9 optimal weight: 20.0000 chunk 13 optimal weight: 20.0000 chunk 65 optimal weight: 1.9990 chunk 4 optimal weight: 0.8980 chunk 53 optimal weight: 1.9990 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 = 0.3197 r_free = 0.3197 target = 0.062922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.056416 restraints weight = 41333.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.057143 restraints weight = 28192.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.057643 restraints weight = 20925.568| |-----------------------------------------------------------------------------| r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5507 Z= 0.185 Angle : 0.413 5.247 7617 Z= 0.244 Chirality : 0.040 0.119 957 Planarity : 0.003 0.039 1037 Dihedral : 3.844 18.344 971 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % 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: 0.62 (0.29), residues: 906 helix: 2.24 (0.25), residues: 441 sheet: -0.66 (0.54), residues: 101 loop : -1.67 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 297 HIS 0.004 0.001 HIS R 296 PHE 0.020 0.002 PHE R 208 TYR 0.011 0.001 TYR A 147 ARG 0.001 0.000 ARG B 22 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1100.94 seconds wall clock time: 20 minutes 42.05 seconds (1242.05 seconds total)