Starting phenix.real_space_refine on Fri Sep 11 16:43:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qog_18537/09_2026/8qog_18537.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qog_18537/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8qog_18537/09_2026/8qog_18537.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qog_18537/09_2026/8qog_18537.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qog_18537/09_2026/8qog_18537.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qog_18537/09_2026/8qog_18537.map" } 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-2.2.1-6174/lib/python3.11/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: 2 Planarities with less than four sites: {'PLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Time building chain proxies: 2.49, per 1000 atoms: 0.24 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: 0.68 Conformation dependent library (CDL) restraints added in 359.2 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: 0.29 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: 1.61 Time building geometry restraints manager: 0.92 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=" O4P PLP C 601 " pdb=" P PLP C 601 " ideal model delta sigma weight residual 1.687 1.608 0.079 2.00e-02 2.50e+03 1.55e+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: 14366 2.88 - 5.76: 113 5.76 - 8.64: 11 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: 6183 25.56 - 51.11: 344 51.11 - 76.67: 34 76.67 - 102.23: 21 102.23 - 127.78: 9 Dihedral angle restraints: 6591 sinusoidal: 2800 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=" 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 dihedral pdb=" C PHE D 54 " pdb=" N PHE D 54 " pdb=" CA PHE D 54 " pdb=" CB PHE D 54 " ideal model delta harmonic sigma weight residual -122.60 -134.02 11.42 0 2.50e+00 1.60e-01 2.09e+01 ... (remaining 6588 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: 2 0.411 - 0.514: 1 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=" 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 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 2.51 2.21 0.31 2.00e-01 2.50e+01 2.37e+00 ... (remaining 1649 not shown) Planarity restraints: 1823 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 PLP C 601 " 0.015 2.00e-02 2.50e+03 9.97e-02 2.48e+02 pdb=" C2A PLP C 601 " 0.049 2.00e-02 2.50e+03 pdb=" C3 PLP C 601 " -0.066 2.00e-02 2.50e+03 pdb=" C4 PLP C 601 " -0.096 2.00e-02 2.50e+03 pdb=" C4A PLP C 601 " 0.237 2.00e-02 2.50e+03 pdb=" C5 PLP C 601 " -0.045 2.00e-02 2.50e+03 pdb=" C5A PLP C 601 " -0.080 2.00e-02 2.50e+03 pdb=" C6 PLP C 601 " 0.035 2.00e-02 2.50e+03 pdb=" N1 PLP C 601 " 0.065 2.00e-02 2.50e+03 pdb=" O3 PLP C 601 " -0.114 2.00e-02 2.50e+03 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 ... (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: 3.280 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.470 Find NCS groups from input model: 0.060 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 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= 0.315 Angle : 0.639 14.396 14496 Z= 0.363 Chirality : 0.047 0.514 1652 Planarity : 0.006 0.130 1823 Dihedral : 16.494 127.781 4151 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/Z covalent geometry : bond 0.00496 / 0.32 (10685) covalent geometry : angle 0.63913 / 0.36 (14496) hydrogen bonds : bond 0.15829 / 10.05 ( 461) hydrogen bonds : angle 5.77170 / 4.30 ( 1338) Misc. bond : bond 0.00073 / 0.05 ( 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 : 0.331 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: 0.1151 time to fit residues: 30.3752 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 : 0.330 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 1.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.5980 chunk 55 optimal weight: 0.1980 chunk 35 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN B 76 GLN B 213 GLN B 295 HIS B 375 GLN C 229 ASN C 334 HIS D 45 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.131702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.107658 restraints weight = 12608.074| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 1.97 r_work: 0.3116 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.3800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 10686 Z= 0.166 Angle : 0.685 10.736 14496 Z= 0.346 Chirality : 0.047 0.202 1652 Planarity : 0.006 0.073 1823 Dihedral : 9.810 115.470 1669 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.42 % Favored : 95.58 % Rotamer: Outliers : 1.13 % Allowed : 8.55 % Favored : 90.31 % 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: 2.10 (0.22), residues: 563 sheet: 1.12 (0.43), residues: 147 loop : -1.48 (0.24), residues: 579 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 437 TYR 0.024 0.002 TYR C 510 PHE 0.021 0.002 PHE B 215 TRP 0.017 0.001 TRP B 100 HIS 0.004 0.001 HIS B 498 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.17 (10685) covalent geometry : angle 0.68483 / 0.35 (14496) hydrogen bonds : bond 0.05636 / 3.86 ( 461) hydrogen bonds : angle 4.32696 / 3.18 ( 1338) Misc. bond : bond 0.00233 / 0.16 ( 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: 13 poor density : 113 time to evaluate : 0.402 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.7876 (tt0) cc_final: 0.6571 (tp40) REVERT: A 60 ASP cc_start: 0.8052 (m-30) cc_final: 0.7562 (m-30) REVERT: A 182 SER cc_start: 0.8274 (t) cc_final: 0.7942 (m) REVERT: C 97 ASP cc_start: 0.8397 (m-30) cc_final: 0.7973 (p0) REVERT: C 147 TYR cc_start: 0.8285 (p90) cc_final: 0.7841 (p90) REVERT: C 158 MET cc_start: 0.8774 (ttm) cc_final: 0.8443 (ttm) REVERT: C 212 ARG cc_start: 0.7674 (OUTLIER) cc_final: 0.7359 (ttp-170) REVERT: C 547 ARG cc_start: 0.7166 (ttp80) cc_final: 0.6924 (ttp-110) outliers start: 13 outliers final: 10 residues processed: 126 average time/residue: 0.0956 time to fit residues: 17.8566 Evaluate side-chains 104 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 93 time to evaluate : 0.305 ------------------------------------------------------------------------------- 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 C residue 413 ILE 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: 2.9990 chunk 39 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 34 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 111 optimal weight: 0.1980 chunk 37 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 42 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.117471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.092664 restraints weight = 13079.285| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 2.02 r_work: 0.2899 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2763 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.5121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 10686 Z= 0.196 Angle : 0.631 7.420 14496 Z= 0.330 Chirality : 0.046 0.210 1652 Planarity : 0.005 0.068 1823 Dihedral : 9.524 125.069 1669 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 1.83 % Allowed : 11.17 % Favored : 87.00 % 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: 0.56 (0.23), residues: 1289 helix: 2.06 (0.22), residues: 564 sheet: 1.16 (0.44), residues: 131 loop : -1.60 (0.23), residues: 594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 280 TYR 0.016 0.002 TYR B 66 PHE 0.020 0.002 PHE D 58 TRP 0.012 0.002 TRP A 104 HIS 0.005 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.20 (10685) covalent geometry : angle 0.63106 / 0.33 (14496) hydrogen bonds : bond 0.07554 / 5.05 ( 461) hydrogen bonds : angle 4.21870 / 3.09 ( 1338) Misc. bond : bond 0.00221 / 0.15 ( 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 123 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 102 time to evaluate : 0.418 Fit side-chains revert: symmetry clash REVERT: A 55 GLN cc_start: 0.8235 (tt0) cc_final: 0.6869 (tp40) REVERT: A 60 ASP cc_start: 0.8178 (m-30) cc_final: 0.7803 (m-30) REVERT: A 147 ASP cc_start: 0.8024 (t0) cc_final: 0.7702 (t0) REVERT: B 98 GLU cc_start: 0.7708 (tp30) cc_final: 0.7497 (tt0) REVERT: B 497 ASP cc_start: 0.7424 (m-30) cc_final: 0.7177 (m-30) REVERT: C 147 TYR cc_start: 0.8479 (p90) cc_final: 0.8015 (p90) REVERT: C 166 LEU cc_start: 0.9157 (OUTLIER) cc_final: 0.8533 (mp) REVERT: C 182 SER cc_start: 0.7734 (t) cc_final: 0.7301 (m) REVERT: C 212 ARG cc_start: 0.7721 (OUTLIER) cc_final: 0.7415 (ttp-170) REVERT: C 217 GLU cc_start: 0.7937 (tp30) cc_final: 0.7517 (tt0) REVERT: C 292 ARG cc_start: 0.7364 (mtp85) cc_final: 0.7078 (mmm160) outliers start: 21 outliers final: 13 residues processed: 119 average time/residue: 0.1102 time to fit residues: 18.2452 Evaluate side-chains 108 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 93 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 166 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 391 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 60 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 101 optimal weight: 0.6980 chunk 2 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 47 optimal weight: 5.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.101155 restraints weight = 12877.207| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.01 r_work: 0.3139 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.5637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10686 Z= 0.152 Angle : 0.561 8.585 14496 Z= 0.293 Chirality : 0.044 0.193 1652 Planarity : 0.005 0.065 1823 Dihedral : 9.029 120.307 1669 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.75 % Allowed : 12.57 % 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: 0.64 (0.24), residues: 1289 helix: 2.20 (0.22), residues: 565 sheet: 1.13 (0.44), residues: 131 loop : -1.62 (0.24), residues: 593 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 547 TYR 0.018 0.002 TYR C 58 PHE 0.012 0.001 PHE D 58 TRP 0.014 0.001 TRP A 104 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.15 (10685) covalent geometry : angle 0.56098 / 0.29 (14496) hydrogen bonds : bond 0.05980 / 4.02 ( 461) hydrogen bonds : angle 4.05794 / 2.97 ( 1338) Misc. bond : bond 0.00057 / 0.04 ( 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 114 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 94 time to evaluate : 0.469 Fit side-chains revert: symmetry clash REVERT: A 147 ASP cc_start: 0.8330 (t0) cc_final: 0.7897 (t0) REVERT: A 209 ILE cc_start: 0.6770 (mt) cc_final: 0.6503 (tt) REVERT: B 497 ASP cc_start: 0.7560 (m-30) cc_final: 0.7266 (m-30) REVERT: C 147 TYR cc_start: 0.8645 (p90) cc_final: 0.8293 (p90) REVERT: C 166 LEU cc_start: 0.9143 (OUTLIER) cc_final: 0.8400 (mp) REVERT: C 182 SER cc_start: 0.7909 (t) cc_final: 0.7443 (m) REVERT: C 217 GLU cc_start: 0.8009 (tp30) cc_final: 0.7627 (tt0) REVERT: C 268 LYS cc_start: 0.7995 (tttm) cc_final: 0.7360 (tppt) REVERT: C 292 ARG cc_start: 0.7529 (mtp85) cc_final: 0.7268 (mtp85) REVERT: C 473 MET cc_start: 0.8507 (mmt) cc_final: 0.8075 (mmt) outliers start: 20 outliers final: 10 residues processed: 110 average time/residue: 0.1153 time to fit residues: 17.7942 Evaluate side-chains 98 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 109 SER Chi-restraints excluded: chain B residue 141 GLN Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 166 LEU 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: 3.9990 chunk 44 optimal weight: 5.9990 chunk 67 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 46 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.555 > 50:) chunk 19 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 116 optimal weight: 4.9990 chunk 85 optimal weight: 0.0170 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 213 GLN C 78 HIS ** C 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.114790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.090590 restraints weight = 13368.100| |-----------------------------------------------------------------------------| r_work (start): 0.2994 rms_B_bonded: 1.88 r_work: 0.2886 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2756 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.6023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 10686 Z= 0.194 Angle : 0.620 8.450 14496 Z= 0.325 Chirality : 0.046 0.217 1652 Planarity : 0.005 0.066 1823 Dihedral : 9.197 117.164 1669 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 2.01 % Allowed : 13.00 % Favored : 84.99 % 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: 0.52 (0.24), residues: 1289 helix: 2.08 (0.22), residues: 565 sheet: 0.99 (0.43), residues: 133 loop : -1.65 (0.23), residues: 591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 547 TYR 0.019 0.002 TYR C 58 PHE 0.016 0.002 PHE C 106 TRP 0.012 0.001 TRP C 294 HIS 0.005 0.001 HIS C 78 Details of bonding type rmsd/Z covalent geometry : bond 0.00477 / 0.19 (10685) covalent geometry : angle 0.61989 / 0.33 (14496) hydrogen bonds : bond 0.07568 / 5.06 ( 461) hydrogen bonds : angle 4.14858 / 3.02 ( 1338) Misc. bond : bond 0.00063 / 0.04 ( 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 112 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 89 time to evaluate : 0.248 Fit side-chains REVERT: A 147 ASP cc_start: 0.8261 (t0) cc_final: 0.7730 (t0) REVERT: A 209 ILE cc_start: 0.6696 (mt) cc_final: 0.6276 (tt) REVERT: B 112 ASP cc_start: 0.7894 (t0) cc_final: 0.7602 (m-30) REVERT: B 497 ASP cc_start: 0.7513 (m-30) cc_final: 0.7176 (m-30) REVERT: C 117 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7272 (mmp80) REVERT: C 147 TYR cc_start: 0.8563 (p90) cc_final: 0.8246 (p90) REVERT: C 182 SER cc_start: 0.7702 (t) cc_final: 0.7264 (m) REVERT: C 217 GLU cc_start: 0.7988 (tp30) cc_final: 0.7624 (tt0) REVERT: C 268 LYS cc_start: 0.7854 (tttm) cc_final: 0.7246 (tppt) REVERT: C 292 ARG cc_start: 0.7566 (mtp85) cc_final: 0.7358 (mtp-110) REVERT: C 547 ARG cc_start: 0.7787 (ttp80) cc_final: 0.7549 (ttp80) outliers start: 23 outliers final: 14 residues processed: 106 average time/residue: 0.1056 time to fit residues: 15.8580 Evaluate side-chains 100 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain B residue 73 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 40 VAL Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 308 GLU 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: 2.9990 chunk 26 optimal weight: 5.9990 chunk 112 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 95 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 100 optimal weight: 0.0060 chunk 5 optimal weight: 0.9980 overall best weight: 0.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.141549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.123447 restraints weight = 12537.700| |-----------------------------------------------------------------------------| r_work (start): 0.3467 rms_B_bonded: 1.23 r_work: 0.3365 rms_B_bonded: 1.93 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.6109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10686 Z= 0.129 Angle : 0.525 7.423 14496 Z= 0.277 Chirality : 0.043 0.190 1652 Planarity : 0.005 0.064 1823 Dihedral : 8.725 116.670 1669 Min Nonbonded Distance : 2.567 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 1.83 % Allowed : 14.22 % 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: 0.73 (0.24), residues: 1289 helix: 2.35 (0.22), residues: 558 sheet: 1.05 (0.43), residues: 133 loop : -1.59 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 547 TYR 0.017 0.001 TYR C 510 PHE 0.011 0.001 PHE B 256 TRP 0.009 0.001 TRP A 104 HIS 0.003 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (10685) covalent geometry : angle 0.52490 / 0.28 (14496) hydrogen bonds : bond 0.05575 / 3.73 ( 461) hydrogen bonds : angle 3.97666 / 2.90 ( 1338) Misc. bond : bond 0.00026 / 0.02 ( 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 104 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 83 time to evaluate : 0.417 Fit side-chains REVERT: A 147 ASP cc_start: 0.8265 (t0) cc_final: 0.7773 (t0) REVERT: C 147 TYR cc_start: 0.8872 (p90) cc_final: 0.8564 (p90) REVERT: C 182 SER cc_start: 0.8398 (t) cc_final: 0.7995 (m) REVERT: C 292 ARG cc_start: 0.8167 (mtp85) cc_final: 0.7937 (mtp180) REVERT: C 547 ARG cc_start: 0.8309 (ttp80) cc_final: 0.8095 (ttp80) outliers start: 21 outliers final: 14 residues processed: 99 average time/residue: 0.1115 time to fit residues: 15.7913 Evaluate side-chains 92 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 78 time to evaluate : 0.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 41 optimal weight: 2.9990 chunk 23 optimal weight: 0.5980 chunk 8 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 67 optimal weight: 0.0010 chunk 113 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 chunk 80 optimal weight: 7.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.141307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.123112 restraints weight = 12376.240| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 1.23 r_work: 0.3396 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.3285 rms_B_bonded: 3.35 restraints_weight: 0.2500 r_work (final): 0.3285 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.6204 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= 0.135 Angle : 0.532 6.105 14496 Z= 0.280 Chirality : 0.043 0.194 1652 Planarity : 0.005 0.063 1823 Dihedral : 8.605 114.770 1669 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.75 % Allowed : 14.40 % 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: 0.77 (0.24), residues: 1289 helix: 2.38 (0.22), residues: 558 sheet: 1.04 (0.44), residues: 133 loop : -1.56 (0.24), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 117 TYR 0.017 0.001 TYR C 510 PHE 0.011 0.001 PHE B 256 TRP 0.008 0.001 TRP C 294 HIS 0.003 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.14 (10685) covalent geometry : angle 0.53188 / 0.28 (14496) hydrogen bonds : bond 0.05778 / 3.86 ( 461) hydrogen bonds : angle 3.95247 / 2.88 ( 1338) Misc. bond : bond 0.00034 / 0.02 ( 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 105 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.425 Fit side-chains REVERT: A 147 ASP cc_start: 0.8298 (t0) cc_final: 0.7793 (t0) REVERT: B 65 LEU cc_start: 0.8458 (tp) cc_final: 0.8212 (tp) REVERT: B 273 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7095 (mt-10) REVERT: C 147 TYR cc_start: 0.8844 (p90) cc_final: 0.8569 (p90) REVERT: C 182 SER cc_start: 0.8413 (t) cc_final: 0.7995 (m) REVERT: C 547 ARG cc_start: 0.8283 (ttp80) cc_final: 0.8069 (ttp80) outliers start: 20 outliers final: 15 residues processed: 100 average time/residue: 0.1131 time to fit residues: 15.9883 Evaluate side-chains 97 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 40 VAL 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=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: 1.9990 chunk 110 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 117 optimal weight: 0.6980 chunk 112 optimal weight: 0.4980 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.4980 chunk 67 optimal weight: 0.5980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3692 r_free = 0.3692 target = 0.142903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.124713 restraints weight = 12372.658| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.23 r_work: 0.3406 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.6248 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 : 0.507 5.973 14496 Z= 0.267 Chirality : 0.042 0.192 1652 Planarity : 0.005 0.060 1823 Dihedral : 8.407 113.662 1669 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.66 % Allowed : 14.40 % 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: 0.83 (0.24), residues: 1289 helix: 2.45 (0.22), residues: 558 sheet: 1.10 (0.44), residues: 133 loop : -1.55 (0.23), residues: 598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 117 TYR 0.017 0.001 TYR C 510 PHE 0.010 0.001 PHE B 256 TRP 0.009 0.001 TRP A 104 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (10685) covalent geometry : angle 0.50712 / 0.27 (14496) hydrogen bonds : bond 0.05196 / 3.47 ( 461) hydrogen bonds : angle 3.90650 / 2.85 ( 1338) Misc. bond : bond 0.00024 / 0.02 ( 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 105 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.416 Fit side-chains REVERT: A 120 MET cc_start: 0.8161 (ttm) cc_final: 0.7804 (mtp) REVERT: A 147 ASP cc_start: 0.8328 (t0) cc_final: 0.7815 (t0) REVERT: B 65 LEU cc_start: 0.8458 (tp) cc_final: 0.8238 (tp) REVERT: B 92 GLU cc_start: 0.6763 (pt0) cc_final: 0.6115 (pm20) REVERT: B 273 GLU cc_start: 0.7552 (mm-30) cc_final: 0.7062 (mt-10) REVERT: C 147 TYR cc_start: 0.8849 (p90) cc_final: 0.8630 (p90) REVERT: C 182 SER cc_start: 0.8360 (t) cc_final: 0.7988 (m) REVERT: C 547 ARG cc_start: 0.8265 (ttp80) cc_final: 0.8064 (ttp80) outliers start: 19 outliers final: 15 residues processed: 102 average time/residue: 0.1125 time to fit residues: 16.3688 Evaluate side-chains 99 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 84 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 160 LEU 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 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: 4.9990 chunk 45 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.2980 chunk 9 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 127 optimal weight: 7.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.136520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.117843 restraints weight = 12582.740| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 1.22 r_work: 0.3347 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3236 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.6325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10686 Z= 0.143 Angle : 0.538 6.539 14496 Z= 0.284 Chirality : 0.043 0.196 1652 Planarity : 0.005 0.061 1823 Dihedral : 8.475 111.225 1669 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.57 % Allowed : 14.14 % Favored : 84.29 % 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: 0.74 (0.24), residues: 1289 helix: 2.36 (0.22), residues: 560 sheet: 1.04 (0.44), residues: 133 loop : -1.59 (0.23), residues: 596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 456 TYR 0.017 0.001 TYR C 510 PHE 0.011 0.001 PHE B 256 TRP 0.009 0.001 TRP C 294 HIS 0.003 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 (10685) covalent geometry : angle 0.53834 / 0.28 (14496) hydrogen bonds : bond 0.05998 / 4.00 ( 461) hydrogen bonds : angle 3.95419 / 2.88 ( 1338) Misc. bond : bond 0.00037 / 0.02 ( 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 104 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 86 time to evaluate : 0.407 Fit side-chains REVERT: A 120 MET cc_start: 0.8264 (ttm) cc_final: 0.7916 (mtp) REVERT: A 147 ASP cc_start: 0.8306 (t0) cc_final: 0.7788 (t0) REVERT: B 65 LEU cc_start: 0.8484 (tp) cc_final: 0.8279 (tp) REVERT: B 92 GLU cc_start: 0.6957 (pt0) cc_final: 0.6253 (pm20) REVERT: B 273 GLU cc_start: 0.7560 (mm-30) cc_final: 0.7086 (mt-10) REVERT: C 182 SER cc_start: 0.8435 (t) cc_final: 0.8025 (m) outliers start: 18 outliers final: 14 residues processed: 104 average time/residue: 0.1126 time to fit residues: 16.5562 Evaluate side-chains 99 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 VAL 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: 0.7980 chunk 52 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 0.9980 chunk 106 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 103 optimal weight: 5.9990 chunk 94 optimal weight: 2.9990 chunk 114 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 62 optimal weight: 0.0070 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.125950 restraints weight = 12244.745| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 1.22 r_work: 0.3417 rms_B_bonded: 1.96 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.6339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 10686 Z= 0.108 Angle : 0.488 5.982 14496 Z= 0.258 Chirality : 0.042 0.187 1652 Planarity : 0.005 0.061 1823 Dihedral : 8.156 110.500 1669 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.48 % Allowed : 14.40 % Favored : 84.12 % 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: 2.52 (0.22), residues: 559 sheet: 1.21 (0.46), residues: 124 loop : -1.45 (0.23), residues: 606 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 0.010 0.001 PHE B 256 TRP 0.008 0.001 TRP C 294 HIS 0.002 0.001 HIS A 122 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.11 (10685) covalent geometry : angle 0.48758 / 0.26 (14496) hydrogen bonds : bond 0.04691 / 3.13 ( 461) hydrogen bonds : angle 3.85275 / 2.81 ( 1338) Misc. bond : bond 0.00019 / 0.01 ( 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 103 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 86 time to evaluate : 0.386 Fit side-chains REVERT: A 120 MET cc_start: 0.8168 (ttm) cc_final: 0.7810 (mtp) REVERT: A 147 ASP cc_start: 0.8312 (t0) cc_final: 0.7787 (t0) REVERT: B 92 GLU cc_start: 0.6894 (pt0) cc_final: 0.6257 (pm20) REVERT: C 97 ASP cc_start: 0.8438 (m-30) cc_final: 0.8114 (p0) REVERT: C 182 SER cc_start: 0.8365 (t) cc_final: 0.8001 (m) outliers start: 17 outliers final: 13 residues processed: 101 average time/residue: 0.1046 time to fit residues: 14.9859 Evaluate side-chains 94 residues out of total 1146 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 81 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 SER 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 424 PHE Chi-restraints excluded: chain C residue 8 THR Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 160 LEU 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: 0.9980 chunk 74 optimal weight: 3.9990 chunk 105 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 chunk 126 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 78 HIS C 96 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.139085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.121102 restraints weight = 12504.174| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.20 r_work: 0.3362 rms_B_bonded: 1.97 restraints_weight: 0.5000 r_work: 0.3249 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.6423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10686 Z= 0.175 Angle : 0.582 7.756 14496 Z= 0.308 Chirality : 0.045 0.210 1652 Planarity : 0.005 0.063 1823 Dihedral : 8.508 107.425 1669 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.57 % Allowed : 14.22 % Favored : 84.21 % 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: 0.67 (0.24), residues: 1289 helix: 2.16 (0.22), residues: 573 sheet: 1.06 (0.44), residues: 132 loop : -1.58 (0.24), residues: 584 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 547 TYR 0.018 0.002 TYR C 485 PHE 0.013 0.001 PHE B 318 TRP 0.010 0.001 TRP C 294 HIS 0.004 0.001 HIS D 45 Details of bonding type rmsd/Z covalent geometry : bond 0.00431 / 0.18 (10685) covalent geometry : angle 0.58156 / 0.31 (14496) hydrogen bonds : bond 0.06756 / 4.51 ( 461) hydrogen bonds : angle 3.98710 / 2.89 ( 1338) Misc. bond : bond 0.00057 / 0.04 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2472.47 seconds wall clock time: 43 minutes 8.37 seconds (2588.37 seconds total)