Starting phenix.real_space_refine on Sun May 3 03:24:15 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.map" model { file = "/net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qog_18537/05_2026/8qog_18537.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.044 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: 5 Type Number sf(0) Gaussians P 1 5.49 5 S 56 5.16 5 C 6712 2.51 5 N 1731 2.21 5 O 1944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10444 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1448 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 7, 'TRANS': 169} Chain: "B" Number of atoms: 3903 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3903 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 24, 'TRANS': 475} Chain: "C" Number of atoms: 4395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 555, 4395 Classifications: {'peptide': 555} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 525} Chain: "D" Number of atoms: 552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 552 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'WAR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 96 Unusual residues: {'PLP': 1, 'Q7G': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 2.40, per 1000 atoms: 0.23 Number of scatterers: 10444 At special positions: 0 Unit cell: (90.552, 95.172, 123.816, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 56 16.00 P 1 15.00 O 1944 8.00 N 1731 7.00 C 6712 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 542.8 milliseconds 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2440 Finding SS restraints... Secondary structure from input PDB file: 53 helices and 7 sheets defined 49.6% alpha, 8.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 57 through 62 Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.706A pdb=" N VAL A 75 " --> pdb=" O ALA A 72 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ASP A 76 " --> pdb=" O THR A 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 72 through 76' Processing helix chain 'A' and resid 82 through 98 removed outlier: 3.926A pdb=" N PHE A 98 " --> pdb=" O PHE A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 123 removed outlier: 3.573A pdb=" N TRP A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N LEU A 123 " --> pdb=" O ILE A 119 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 145 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 152 through 170 Proline residue: A 162 - end of helix Processing helix chain 'A' and resid 171 through 173 No H-bonds generated for 'chain 'A' and resid 171 through 173' Processing helix chain 'A' and resid 176 through 192 Processing helix chain 'B' and resid 55 through 72 Processing helix chain 'B' and resid 89 through 91 No H-bonds generated for 'chain 'B' and resid 89 through 91' Processing helix chain 'B' and resid 92 through 100 removed outlier: 3.838A pdb=" N LEU B 96 " --> pdb=" O GLU B 92 " (cutoff:3.500A) Processing helix chain 'B' and resid 115 through 120 removed outlier: 3.870A pdb=" N ALA B 119 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 120 " --> pdb=" O TRP B 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 115 through 120' Processing helix chain 'B' and resid 161 through 176 Processing helix chain 'B' and resid 191 through 203 Processing helix chain 'B' and resid 213 through 216 Processing helix chain 'B' and resid 217 through 222 Processing helix chain 'B' and resid 223 through 226 removed outlier: 3.582A pdb=" N THR B 226 " --> pdb=" O PRO B 223 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 223 through 226' Processing helix chain 'B' and resid 239 through 250 removed outlier: 4.023A pdb=" N ARG B 250 " --> pdb=" O LEU B 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 279 removed outlier: 3.511A pdb=" N LEU B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 314 Processing helix chain 'B' and resid 334 through 339 removed outlier: 3.786A pdb=" N HIS B 338 " --> pdb=" O GLY B 334 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N PHE B 339 " --> pdb=" O LEU B 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 334 through 339' Processing helix chain 'B' and resid 342 through 347 removed outlier: 3.649A pdb=" N ILE B 347 " --> pdb=" O ARG B 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 368 through 379 removed outlier: 4.120A pdb=" N ILE B 377 " --> pdb=" O LEU B 373 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N SER B 379 " --> pdb=" O GLN B 375 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 384 Processing helix chain 'B' and resid 389 through 406 removed outlier: 4.010A pdb=" N VAL B 393 " --> pdb=" O PRO B 389 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 426 removed outlier: 4.065A pdb=" N GLN B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N SER B 426 " --> pdb=" O ASP B 422 " (cutoff:3.500A) Processing helix chain 'B' and resid 450 through 458 Processing helix chain 'B' and resid 461 through 476 Processing helix chain 'B' and resid 482 through 504 removed outlier: 3.575A pdb=" N GLU B 486 " --> pdb=" O ILE B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 553 Processing helix chain 'C' and resid 19 through 28 Processing helix chain 'C' and resid 57 through 86 removed outlier: 4.078A pdb=" N SER C 61 " --> pdb=" O PRO C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 107 No H-bonds generated for 'chain 'C' and resid 105 through 107' Processing helix chain 'C' and resid 108 through 114 Processing helix chain 'C' and resid 118 through 122 Processing helix chain 'C' and resid 173 through 186 Processing helix chain 'C' and resid 200 through 215 removed outlier: 3.553A pdb=" N ILE C 204 " --> pdb=" O THR C 200 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 231 removed outlier: 3.650A pdb=" N ASN C 229 " --> pdb=" O GLY C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 236 removed outlier: 3.559A pdb=" N PHE C 236 " --> pdb=" O PHE C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 250 through 261 removed outlier: 3.535A pdb=" N ARG C 254 " --> pdb=" O HIS C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 271 through 286 removed outlier: 3.713A pdb=" N VAL C 284 " --> pdb=" O ARG C 280 " (cutoff:3.500A) Processing helix chain 'C' and resid 313 through 325 removed outlier: 3.572A pdb=" N LEU C 317 " --> pdb=" O ASN C 313 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 351 Processing helix chain 'C' and resid 378 through 389 removed outlier: 3.812A pdb=" N LEU C 387 " --> pdb=" O ASP C 383 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 395 Processing helix chain 'C' and resid 399 through 415 Processing helix chain 'C' and resid 421 through 444 removed outlier: 3.593A pdb=" N GLY C 444 " --> pdb=" O LEU C 440 " (cutoff:3.500A) Processing helix chain 'C' and resid 464 through 476 removed outlier: 4.014A pdb=" N ALA C 468 " --> pdb=" O SER C 464 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE C 469 " --> pdb=" O LYS C 465 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER C 470 " --> pdb=" O MET C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 523 Processing helix chain 'C' and resid 541 through 553 Proline residue: C 550 - end of helix Processing helix chain 'D' and resid 29 through 42 Processing helix chain 'D' and resid 50 through 68 removed outlier: 3.773A pdb=" N PHE D 54 " --> pdb=" O LEU D 50 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 52 Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124 removed outlier: 6.273A pdb=" N ILE B 133 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN B 146 " --> pdb=" O ILE B 133 " (cutoff:3.500A) removed outlier: 8.268A pdb=" N LEU B 506 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N PHE B 148 " --> pdb=" O LEU B 506 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211 removed outlier: 3.623A pdb=" N THR B 350 " --> pdb=" O LEU B 366 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N PHE B 318 " --> pdb=" O LYS B 286 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ILE B 288 " --> pdb=" O PHE B 318 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ASP B 320 " --> pdb=" O ILE B 288 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N THR B 290 " --> pdb=" O ASP B 320 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N VAL B 231 " --> pdb=" O PHE B 287 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N VAL B 289 " --> pdb=" O VAL B 231 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N VAL B 233 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 9.146A pdb=" N GLU B 291 " --> pdb=" O VAL B 233 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N ASP B 235 " --> pdb=" O GLU B 291 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N PHE B 256 " --> pdb=" O ALA B 234 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436 removed outlier: 3.685A pdb=" N THR B 508 " --> pdb=" O LYS B 526 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 126 through 127 removed outlier: 3.923A pdb=" N ARG C 135 " --> pdb=" O THR C 127 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ALA C 153 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N ILE C 140 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N SER C 151 " --> pdb=" O ILE C 140 " (cutoff:3.500A) removed outlier: 7.525A pdb=" N HIS C 142 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N THR C 149 " --> pdb=" O HIS C 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222 removed outlier: 4.482A pdb=" N THR C 363 " --> pdb=" O GLU C 332 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N ILE C 297 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 7.952A pdb=" N PHE C 329 " --> pdb=" O ILE C 297 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE C 299 " --> pdb=" O PHE C 329 " (cutoff:3.500A) removed outlier: 7.849A pdb=" N ASP C 331 " --> pdb=" O ILE C 299 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ALA C 301 " --> pdb=" O ASP C 331 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP C 246 " --> pdb=" O CYS C 300 " (cutoff:3.500A) removed outlier: 8.147A pdb=" N GLU C 302 " --> pdb=" O ASP C 246 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N VAL C 243 " --> pdb=" O ARG C 265 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N PHE C 267 " --> pdb=" O VAL C 243 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N SER C 245 " --> pdb=" O PHE C 267 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 459 removed outlier: 4.166A pdb=" N VAL C 481 " --> pdb=" O ARG C 496 " (cutoff:3.500A) 461 hydrogen bonds defined for protein. 1338 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: 1.56 Time building geometry restraints manager: 1.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3172 1.34 - 1.46: 1976 1.46 - 1.58: 5448 1.58 - 1.70: 2 1.70 - 1.82: 87 Bond restraints: 10685 Sorted by residual: bond pdb=" N PRO B 75 " pdb=" CD PRO B 75 " ideal model delta sigma weight residual 1.473 1.824 -0.351 1.40e-02 5.10e+03 6.28e+02 bond pdb=" C15 WAR A 301 " pdb=" O49 WAR A 301 " ideal model delta sigma weight residual 1.448 1.363 0.085 2.00e-02 2.50e+03 1.81e+01 bond pdb=" CA LEU D 50 " pdb=" C LEU D 50 " ideal model delta sigma weight residual 1.524 1.570 -0.046 1.25e-02 6.40e+03 1.34e+01 bond pdb=" N TYR D 49 " pdb=" CA TYR D 49 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.16e+01 bond pdb=" N PHE D 54 " pdb=" CA PHE D 54 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.21e-02 6.83e+03 1.08e+01 ... (remaining 10680 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 14377 2.88 - 5.76: 105 5.76 - 8.64: 8 8.64 - 11.52: 4 11.52 - 14.40: 2 Bond angle restraints: 14496 Sorted by residual: angle pdb=" N MET D 51 " pdb=" CA MET D 51 " pdb=" C MET D 51 " ideal model delta sigma weight residual 113.28 98.88 14.40 1.22e+00 6.72e-01 1.39e+02 angle pdb=" C SER D 53 " pdb=" N PHE D 54 " pdb=" CA PHE D 54 " ideal model delta sigma weight residual 120.28 109.26 11.02 1.34e+00 5.57e-01 6.76e+01 angle pdb=" CA PRO B 90 " pdb=" N PRO B 90 " pdb=" CD PRO B 90 " ideal model delta sigma weight residual 112.00 102.06 9.94 1.40e+00 5.10e-01 5.04e+01 angle pdb=" CA PRO B 75 " pdb=" N PRO B 75 " pdb=" CD PRO B 75 " ideal model delta sigma weight residual 112.00 102.08 9.92 1.40e+00 5.10e-01 5.02e+01 angle pdb=" N PRO B 75 " pdb=" CA PRO B 75 " pdb=" CB PRO B 75 " ideal model delta sigma weight residual 103.25 109.02 -5.77 1.05e+00 9.07e-01 3.02e+01 ... (remaining 14491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.56: 6189 25.56 - 51.11: 342 51.11 - 76.67: 29 76.67 - 102.23: 18 102.23 - 127.78: 10 Dihedral angle restraints: 6588 sinusoidal: 2797 harmonic: 3791 Sorted by residual: dihedral pdb=" C TYR D 49 " pdb=" N TYR D 49 " pdb=" CA TYR D 49 " pdb=" CB TYR D 49 " ideal model delta harmonic sigma weight residual -122.60 -138.80 16.20 0 2.50e+00 1.60e-01 4.20e+01 dihedral pdb=" C5A PLP C 601 " pdb=" O4P PLP C 601 " pdb=" P PLP C 601 " pdb=" O1P PLP C 601 " ideal model delta sinusoidal sigma weight residual 76.43 -167.37 -116.20 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" N TYR D 49 " pdb=" C TYR D 49 " pdb=" CA TYR D 49 " pdb=" CB TYR D 49 " ideal model delta harmonic sigma weight residual 122.80 135.20 -12.40 0 2.50e+00 1.60e-01 2.46e+01 ... (remaining 6585 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1591 0.103 - 0.205: 53 0.205 - 0.308: 5 0.308 - 0.411: 1 0.411 - 0.514: 2 Chirality restraints: 1652 Sorted by residual: chirality pdb=" CA TYR D 49 " pdb=" N TYR D 49 " pdb=" C TYR D 49 " pdb=" CB TYR D 49 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" C15 WAR A 301 " pdb=" C14 WAR A 301 " pdb=" C16 WAR A 301 " pdb=" O49 WAR A 301 " both_signs ideal model delta sigma weight residual False 2.69 2.21 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CA PHE D 54 " pdb=" N PHE D 54 " pdb=" C PHE D 54 " pdb=" CB PHE D 54 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 1649 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C11 Q7G C 602 " 0.017 2.00e-02 2.50e+03 5.95e-02 4.42e+01 pdb=" C13 Q7G C 602 " 0.006 2.00e-02 2.50e+03 pdb=" C14 Q7G C 602 " 0.099 2.00e-02 2.50e+03 pdb=" C15 Q7G C 602 " -0.071 2.00e-02 2.50e+03 pdb=" C16 Q7G C 602 " -0.050 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 89 " -0.091 5.00e-02 4.00e+02 1.30e-01 2.72e+01 pdb=" N PRO B 90 " 0.225 5.00e-02 4.00e+02 pdb=" CA PRO B 90 " -0.066 5.00e-02 4.00e+02 pdb=" CD PRO B 90 " -0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE D 48 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C PHE D 48 " -0.060 2.00e-02 2.50e+03 pdb=" O PHE D 48 " 0.023 2.00e-02 2.50e+03 pdb=" N TYR D 49 " 0.020 2.00e-02 2.50e+03 ... (remaining 1820 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1803 2.77 - 3.30: 9217 3.30 - 3.84: 15766 3.84 - 4.37: 17162 4.37 - 4.90: 33208 Nonbonded interactions: 77156 Sorted by model distance: nonbonded pdb=" OE1 GLN B 213 " pdb=" OG SER C 395 " model vdw 2.240 3.040 nonbonded pdb=" O PHE D 67 " pdb=" C SER D 68 " model vdw 2.291 3.270 nonbonded pdb=" OD1 ASN D 21 " pdb=" N GLY D 22 " model vdw 2.328 3.120 nonbonded pdb=" OD1 ASP A 60 " pdb=" NH1 ARG B 228 " model vdw 2.331 3.120 nonbonded pdb=" OD1 ASP B 428 " pdb=" NH1 ARG B 431 " model vdw 2.386 3.120 ... (remaining 77151 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 9.910 Find NCS groups from input model: 0.050 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: 0.010 Load rotamer database and sin/cos tables:1.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6868 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 : 0.005 0.351 10686 Z= 0.319 Angle : 0.625 14.396 14496 Z= 0.360 Chirality : 0.048 0.514 1652 Planarity : 0.005 0.130 1823 Dihedral : 16.354 127.781 4148 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.35 % Allowed : 0.35 % Favored : 99.30 % Cbeta Deviations : 0.16 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.24), residues: 1289 helix: 2.48 (0.23), residues: 543 sheet: 1.33 (0.45), residues: 141 loop : -1.34 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 292 TYR 0.025 0.001 TYR D 49 PHE 0.025 0.001 PHE D 62 TRP 0.006 0.001 TRP C 294 HIS 0.003 0.001 HIS B 498 Details of bonding type rmsd covalent geometry : bond 0.00505 (10685) covalent geometry : angle 0.62501 (14496) hydrogen bonds : bond 0.15829 ( 461) hydrogen bonds : angle 5.77170 ( 1338) Misc. bond : bond 0.00073 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 187 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7090 (tt0) cc_final: 0.5962 (tp40) REVERT: C 135 ARG cc_start: 0.7504 (mtm180) cc_final: 0.7214 (mtm-85) REVERT: C 521 LYS cc_start: 0.7281 (tttt) cc_final: 0.7055 (ttmm) outliers start: 4 outliers final: 0 residues processed: 190 average time/residue: 0.1107 time to fit residues: 29.0427 Evaluate side-chains 105 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.4980 chunk 55 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 76 GLN B 213 GLN B 295 HIS C 229 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.129081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.104954 restraints weight = 12678.300| |-----------------------------------------------------------------------------| r_work (start): 0.3166 rms_B_bonded: 1.97 r_work: 0.3057 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2925 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2925 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 10686 Z= 0.189 Angle : 0.685 10.636 14496 Z= 0.349 Chirality : 0.047 0.210 1652 Planarity : 0.006 0.073 1823 Dihedral : 9.143 120.640 1666 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.05 % Allowed : 8.20 % Favored : 90.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1289 helix: 2.17 (0.22), residues: 559 sheet: 1.23 (0.45), residues: 135 loop : -1.52 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 428 TYR 0.024 0.002 TYR C 510 PHE 0.022 0.002 PHE C 106 TRP 0.013 0.002 TRP B 100 HIS 0.005 0.001 HIS D 60 Details of bonding type rmsd covalent geometry : bond 0.00427 (10685) covalent geometry : angle 0.68498 (14496) hydrogen bonds : bond 0.06281 ( 461) hydrogen bonds : angle 4.39921 ( 1338) Misc. bond : bond 0.00006 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 114 time to evaluate : 0.293 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7889 (tt0) cc_final: 0.6587 (tp40) REVERT: A 60 ASP cc_start: 0.8109 (m-30) cc_final: 0.7681 (m-30) REVERT: A 147 ASP cc_start: 0.7953 (t0) cc_final: 0.7736 (t0) REVERT: A 182 SER cc_start: 0.8287 (t) cc_final: 0.7977 (m) REVERT: C 97 ASP cc_start: 0.8350 (m-30) cc_final: 0.7972 (p0) REVERT: C 147 TYR cc_start: 0.8277 (p90) cc_final: 0.7901 (p90) REVERT: C 158 MET cc_start: 0.8782 (ttm) cc_final: 0.8515 (ttm) REVERT: C 212 ARG cc_start: 0.7725 (OUTLIER) cc_final: 0.7417 (ttp-170) REVERT: C 547 ARG cc_start: 0.7185 (ttp80) cc_final: 0.6950 (ttp-110) outliers start: 12 outliers final: 9 residues processed: 125 average time/residue: 0.0957 time to fit residues: 17.3750 Evaluate side-chains 103 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 297 SER Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 0.4980 chunk 42 optimal weight: 0.6980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 GLN B 243 GLN C 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.115629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.091318 restraints weight = 13310.625| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 1.90 r_work: 0.3122 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.5506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 10686 Z= 0.217 Angle : 0.673 8.693 14496 Z= 0.351 Chirality : 0.048 0.215 1652 Planarity : 0.006 0.067 1823 Dihedral : 8.975 125.727 1666 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.66 % Allowed : 12.30 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.23), residues: 1289 helix: 1.84 (0.22), residues: 572 sheet: 0.96 (0.43), residues: 133 loop : -1.66 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 250 TYR 0.021 0.002 TYR C 58 PHE 0.022 0.002 PHE D 58 TRP 0.015 0.002 TRP A 104 HIS 0.003 0.001 HIS C 269 Details of bonding type rmsd covalent geometry : bond 0.00532 (10685) covalent geometry : angle 0.67273 (14496) hydrogen bonds : bond 0.08432 ( 461) hydrogen bonds : angle 4.36232 ( 1338) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 96 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 60 ASP cc_start: 0.8429 (m-30) cc_final: 0.8129 (m-30) REVERT: A 147 ASP cc_start: 0.8304 (t0) cc_final: 0.7849 (t0) REVERT: A 209 ILE cc_start: 0.7070 (mt) cc_final: 0.6748 (tt) REVERT: B 497 ASP cc_start: 0.7749 (m-30) cc_final: 0.7535 (m-30) REVERT: C 147 TYR cc_start: 0.8771 (p90) cc_final: 0.8344 (p90) REVERT: C 182 SER cc_start: 0.8045 (t) cc_final: 0.7611 (m) REVERT: C 212 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7630 (ttp-170) REVERT: C 217 GLU cc_start: 0.8075 (tp30) cc_final: 0.7793 (tt0) REVERT: C 292 ARG cc_start: 0.7755 (mtp85) cc_final: 0.7537 (mtp85) REVERT: C 339 MET cc_start: 0.9054 (mtp) cc_final: 0.8811 (mtp) REVERT: C 361 MET cc_start: 0.8124 (ttp) cc_final: 0.7898 (ttp) outliers start: 19 outliers final: 11 residues processed: 111 average time/residue: 0.1174 time to fit residues: 17.7437 Evaluate side-chains 99 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 212 ARG Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 335 SER Chi-restraints excluded: chain C residue 357 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 46 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 101 optimal weight: 3.9990 chunk 2 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.117809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.093583 restraints weight = 13235.671| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 1.90 r_work: 0.2908 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.5738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10686 Z= 0.147 Angle : 0.558 6.973 14496 Z= 0.293 Chirality : 0.044 0.198 1652 Planarity : 0.005 0.063 1823 Dihedral : 8.384 121.529 1666 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.57 % Allowed : 12.74 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.24), residues: 1289 helix: 2.11 (0.22), residues: 565 sheet: 1.07 (0.43), residues: 131 loop : -1.67 (0.23), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 547 TYR 0.019 0.002 TYR C 510 PHE 0.013 0.001 PHE C 106 TRP 0.012 0.001 TRP A 104 HIS 0.003 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00346 (10685) covalent geometry : angle 0.55762 (14496) hydrogen bonds : bond 0.06191 ( 461) hydrogen bonds : angle 4.11889 ( 1338) Misc. bond : bond 0.00010 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 91 time to evaluate : 0.430 Fit side-chains REVERT: A 147 ASP cc_start: 0.8195 (t0) cc_final: 0.7682 (t0) REVERT: A 209 ILE cc_start: 0.6509 (mt) cc_final: 0.6192 (tt) REVERT: B 112 ASP cc_start: 0.7833 (t0) cc_final: 0.7467 (m-30) REVERT: B 126 GLU cc_start: 0.8287 (mt-10) cc_final: 0.8074 (mt-10) REVERT: B 497 ASP cc_start: 0.7211 (m-30) cc_final: 0.6834 (m-30) REVERT: C 117 ARG cc_start: 0.7624 (mpt180) cc_final: 0.7159 (mmp80) REVERT: C 147 TYR cc_start: 0.8416 (p90) cc_final: 0.8089 (p90) REVERT: C 182 SER cc_start: 0.7540 (t) cc_final: 0.7098 (m) REVERT: C 217 GLU cc_start: 0.7904 (tp30) cc_final: 0.7531 (tt0) REVERT: C 268 LYS cc_start: 0.7700 (tttm) cc_final: 0.7039 (tppt) REVERT: C 292 ARG cc_start: 0.7368 (mtp85) cc_final: 0.7122 (mtp85) REVERT: C 339 MET cc_start: 0.8906 (mtp) cc_final: 0.8649 (mtp) REVERT: C 361 MET cc_start: 0.7791 (ttp) cc_final: 0.7516 (ttp) outliers start: 18 outliers final: 11 residues processed: 105 average time/residue: 0.1125 time to fit residues: 16.4140 Evaluate side-chains 96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 85 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.9980 chunk 46 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 116 optimal weight: 4.9990 chunk 85 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS C 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.118674 restraints weight = 12599.864| |-----------------------------------------------------------------------------| r_work (start): 0.3404 rms_B_bonded: 1.24 r_work: 0.3300 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3188 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.6102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10686 Z= 0.212 Angle : 0.638 9.009 14496 Z= 0.334 Chirality : 0.047 0.223 1652 Planarity : 0.006 0.067 1823 Dihedral : 8.513 118.176 1666 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.01 % Allowed : 13.53 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.35 (0.23), residues: 1289 helix: 1.89 (0.22), residues: 572 sheet: 0.96 (0.48), residues: 108 loop : -1.63 (0.23), residues: 609 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 250 TYR 0.019 0.002 TYR C 510 PHE 0.015 0.002 PHE D 58 TRP 0.012 0.001 TRP A 104 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00528 (10685) covalent geometry : angle 0.63780 (14496) hydrogen bonds : bond 0.07885 ( 461) hydrogen bonds : angle 4.21217 ( 1338) Misc. bond : bond 0.00013 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 86 time to evaluate : 0.346 Fit side-chains REVERT: A 147 ASP cc_start: 0.8293 (t0) cc_final: 0.7787 (t0) REVERT: A 154 THR cc_start: 0.8329 (OUTLIER) cc_final: 0.8028 (m) REVERT: A 209 ILE cc_start: 0.7495 (mt) cc_final: 0.7156 (tt) REVERT: C 147 TYR cc_start: 0.8904 (p90) cc_final: 0.8602 (p90) REVERT: C 182 SER cc_start: 0.8373 (t) cc_final: 0.7963 (m) REVERT: C 268 LYS cc_start: 0.8376 (tttm) cc_final: 0.8053 (tppt) outliers start: 23 outliers final: 14 residues processed: 105 average time/residue: 0.1065 time to fit residues: 15.8553 Evaluate side-chains 95 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 375 ILE Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 94 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 0.6980 chunk 39 optimal weight: 0.5980 chunk 80 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 196 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.142298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.124429 restraints weight = 12478.122| |-----------------------------------------------------------------------------| r_work (start): 0.3482 rms_B_bonded: 1.20 r_work: 0.3380 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3272 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.6127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10686 Z= 0.119 Angle : 0.514 7.667 14496 Z= 0.272 Chirality : 0.042 0.199 1652 Planarity : 0.005 0.064 1823 Dihedral : 7.925 117.650 1666 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.83 % Allowed : 14.57 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.24), residues: 1289 helix: 2.25 (0.22), residues: 564 sheet: 1.10 (0.43), residues: 132 loop : -1.60 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 117 TYR 0.017 0.001 TYR C 510 PHE 0.011 0.001 PHE B 256 TRP 0.010 0.001 TRP C 294 HIS 0.002 0.001 HIS C 78 Details of bonding type rmsd covalent geometry : bond 0.00264 (10685) covalent geometry : angle 0.51424 (14496) hydrogen bonds : bond 0.05236 ( 461) hydrogen bonds : angle 3.98378 ( 1338) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 80 time to evaluate : 0.353 Fit side-chains REVERT: A 147 ASP cc_start: 0.8233 (t0) cc_final: 0.7741 (t0) REVERT: C 147 TYR cc_start: 0.8872 (p90) cc_final: 0.8594 (p90) REVERT: C 182 SER cc_start: 0.8361 (t) cc_final: 0.7946 (m) outliers start: 21 outliers final: 15 residues processed: 96 average time/residue: 0.1037 time to fit residues: 14.1571 Evaluate side-chains 92 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 208 LYS Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 504 THR Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.0670 chunk 113 optimal weight: 0.3980 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 0.5980 chunk 80 optimal weight: 0.7980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.144985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.126941 restraints weight = 12300.149| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.27 r_work: 0.3355 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.3248 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.3248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.6149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 10686 Z= 0.102 Angle : 0.486 6.640 14496 Z= 0.256 Chirality : 0.041 0.206 1652 Planarity : 0.005 0.063 1823 Dihedral : 7.536 115.692 1666 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.75 % Allowed : 14.49 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.24), residues: 1289 helix: 2.42 (0.22), residues: 564 sheet: 1.24 (0.44), residues: 130 loop : -1.52 (0.23), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 117 TYR 0.017 0.001 TYR C 510 PHE 0.010 0.001 PHE B 256 TRP 0.010 0.001 TRP C 294 HIS 0.002 0.000 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00218 (10685) covalent geometry : angle 0.48599 (14496) hydrogen bonds : bond 0.04427 ( 461) hydrogen bonds : angle 3.87810 ( 1338) Misc. bond : bond 0.00003 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 80 time to evaluate : 0.354 Fit side-chains REVERT: A 147 ASP cc_start: 0.8271 (t0) cc_final: 0.7733 (t0) REVERT: A 154 THR cc_start: 0.8068 (OUTLIER) cc_final: 0.7732 (m) REVERT: B 65 LEU cc_start: 0.8190 (tp) cc_final: 0.7942 (tp) REVERT: C 97 ASP cc_start: 0.8375 (m-30) cc_final: 0.7968 (p0) REVERT: C 147 TYR cc_start: 0.8750 (p90) cc_final: 0.8518 (p90) REVERT: C 182 SER cc_start: 0.8200 (t) cc_final: 0.7798 (m) outliers start: 20 outliers final: 12 residues processed: 98 average time/residue: 0.1028 time to fit residues: 14.3497 Evaluate side-chains 90 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 77 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 391 THR Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 92 optimal weight: 5.9990 chunk 94 optimal weight: 3.9990 chunk 97 optimal weight: 4.9990 chunk 118 optimal weight: 0.8980 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN C 78 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.143861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125723 restraints weight = 12339.285| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.23 r_work: 0.3324 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.6223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10686 Z= 0.123 Angle : 0.513 6.062 14496 Z= 0.270 Chirality : 0.042 0.197 1652 Planarity : 0.005 0.063 1823 Dihedral : 7.496 113.622 1666 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 1.66 % Allowed : 14.75 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.24), residues: 1289 helix: 2.43 (0.22), residues: 564 sheet: 1.29 (0.46), residues: 123 loop : -1.46 (0.23), residues: 602 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 456 TYR 0.018 0.001 TYR C 510 PHE 0.010 0.001 PHE B 256 TRP 0.009 0.001 TRP C 294 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00284 (10685) covalent geometry : angle 0.51304 (14496) hydrogen bonds : bond 0.05261 ( 461) hydrogen bonds : angle 3.89750 ( 1338) Misc. bond : bond 0.00001 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 82 time to evaluate : 0.404 Fit side-chains REVERT: A 120 MET cc_start: 0.7985 (ttm) cc_final: 0.7637 (mtp) REVERT: A 147 ASP cc_start: 0.8251 (t0) cc_final: 0.7727 (t0) REVERT: A 154 THR cc_start: 0.8125 (OUTLIER) cc_final: 0.7841 (m) REVERT: B 65 LEU cc_start: 0.8239 (tp) cc_final: 0.8000 (tp) REVERT: C 97 ASP cc_start: 0.8375 (m-30) cc_final: 0.7957 (p0) REVERT: C 147 TYR cc_start: 0.8823 (p90) cc_final: 0.8598 (p90) REVERT: C 182 SER cc_start: 0.8203 (t) cc_final: 0.7803 (m) outliers start: 19 outliers final: 13 residues processed: 97 average time/residue: 0.1035 time to fit residues: 14.2004 Evaluate side-chains 93 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 79 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 0.0770 chunk 9 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.9990 chunk 127 optimal weight: 7.9990 overall best weight: 0.7342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.144377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.126267 restraints weight = 12346.297| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 1.23 r_work: 0.3397 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3286 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 10686 Z= 0.111 Angle : 0.495 5.999 14496 Z= 0.261 Chirality : 0.042 0.198 1652 Planarity : 0.005 0.061 1823 Dihedral : 7.327 112.212 1666 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.22 % Allowed : 15.01 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.94 (0.24), residues: 1289 helix: 2.40 (0.22), residues: 571 sheet: 1.34 (0.46), residues: 123 loop : -1.43 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 547 TYR 0.017 0.001 TYR C 510 PHE 0.010 0.001 PHE B 256 TRP 0.009 0.001 TRP C 294 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00252 (10685) covalent geometry : angle 0.49454 (14496) hydrogen bonds : bond 0.04712 ( 461) hydrogen bonds : angle 3.86832 ( 1338) Misc. bond : bond 0.00002 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.413 Fit side-chains REVERT: A 120 MET cc_start: 0.8186 (ttm) cc_final: 0.7818 (mtp) REVERT: A 147 ASP cc_start: 0.8270 (t0) cc_final: 0.7762 (t0) REVERT: A 154 THR cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (m) REVERT: B 65 LEU cc_start: 0.8486 (tp) cc_final: 0.8277 (tp) REVERT: B 92 GLU cc_start: 0.6818 (pt0) cc_final: 0.6228 (pm20) REVERT: B 273 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7094 (mt-10) REVERT: C 97 ASP cc_start: 0.8422 (m-30) cc_final: 0.8117 (p0) REVERT: C 147 TYR cc_start: 0.8872 (p90) cc_final: 0.8648 (p90) REVERT: C 182 SER cc_start: 0.8375 (t) cc_final: 0.8022 (m) outliers start: 14 outliers final: 12 residues processed: 94 average time/residue: 0.1028 time to fit residues: 13.6827 Evaluate side-chains 92 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain B residue 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 74 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 106 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 103 optimal weight: 2.9990 chunk 94 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 62 optimal weight: 5.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 64 GLN B 213 GLN C 78 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.139553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.121644 restraints weight = 12337.847| |-----------------------------------------------------------------------------| r_work (start): 0.3449 rms_B_bonded: 1.19 r_work: 0.3346 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.3241 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.3241 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8362 moved from start: 0.6368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 10686 Z= 0.168 Angle : 0.578 7.609 14496 Z= 0.305 Chirality : 0.045 0.204 1652 Planarity : 0.005 0.062 1823 Dihedral : 7.588 110.177 1666 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.48 % Allowed : 14.66 % Favored : 83.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.24), residues: 1289 helix: 2.28 (0.22), residues: 567 sheet: 1.15 (0.44), residues: 132 loop : -1.56 (0.24), residues: 590 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 547 TYR 0.019 0.002 TYR C 510 PHE 0.013 0.001 PHE B 318 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd covalent geometry : bond 0.00413 (10685) covalent geometry : angle 0.57756 (14496) hydrogen bonds : bond 0.06575 ( 461) hydrogen bonds : angle 3.98684 ( 1338) Misc. bond : bond 0.00007 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2578 Ramachandran restraints generated. 1289 Oldfield, 0 Emsley, 1289 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 81 time to evaluate : 0.359 Fit side-chains REVERT: A 120 MET cc_start: 0.8344 (ttm) cc_final: 0.7966 (mtp) REVERT: A 147 ASP cc_start: 0.8248 (t0) cc_final: 0.7757 (t0) REVERT: A 154 THR cc_start: 0.8248 (OUTLIER) cc_final: 0.7979 (m) REVERT: B 65 LEU cc_start: 0.8509 (tp) cc_final: 0.8303 (tp) REVERT: B 92 GLU cc_start: 0.6999 (pt0) cc_final: 0.6354 (pm20) REVERT: C 97 ASP cc_start: 0.8408 (m-30) cc_final: 0.8129 (p0) REVERT: C 147 TYR cc_start: 0.8895 (p90) cc_final: 0.8646 (p90) REVERT: C 182 SER cc_start: 0.8389 (t) cc_final: 0.7989 (m) outliers start: 17 outliers final: 13 residues processed: 97 average time/residue: 0.1018 time to fit residues: 14.0976 Evaluate side-chains 94 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 154 THR Chi-restraints excluded: chain B residue 136 THR Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 371 MET Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 199 THR Chi-restraints excluded: chain C residue 308 GLU Chi-restraints excluded: chain C residue 458 LEU Chi-restraints excluded: chain C residue 495 VAL Chi-restraints excluded: chain C residue 560 VAL Chi-restraints excluded: chain D residue 41 THR Chi-restraints excluded: chain D residue 61 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 120 optimal weight: 0.4980 chunk 74 optimal weight: 2.9990 chunk 105 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 126 optimal weight: 0.0870 chunk 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.144002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125854 restraints weight = 12375.084| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.23 r_work: 0.3423 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3306 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.3306 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 10686 Z= 0.106 Angle : 0.495 5.874 14496 Z= 0.263 Chirality : 0.042 0.195 1652 Planarity : 0.005 0.063 1823 Dihedral : 7.269 110.396 1666 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 1.31 % Allowed : 14.75 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.24), residues: 1289 helix: 2.38 (0.22), residues: 571 sheet: 1.31 (0.46), residues: 123 loop : -1.43 (0.24), residues: 595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 547 TYR 0.017 0.001 TYR C 510 PHE 0.015 0.001 PHE B 185 TRP 0.009 0.001 TRP C 294 HIS 0.002 0.001 HIS C 514 Details of bonding type rmsd covalent geometry : bond 0.00234 (10685) covalent geometry : angle 0.49466 (14496) hydrogen bonds : bond 0.04565 ( 461) hydrogen bonds : angle 3.86610 ( 1338) Misc. bond : bond 0.00010 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2383.55 seconds wall clock time: 41 minutes 38.54 seconds (2498.54 seconds total)