Starting phenix.real_space_refine on Tue Jan 21 20:05:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.map" model { file = "/net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9au7_43872/01_2025/9au7_43872.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.019 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 S 56 5.16 5 C 5544 2.51 5 N 1436 2.21 5 O 1565 1.98 5 H 8703 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 17304 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 9679 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 24, 'TRANS': 572} Chain breaks: 5 Chain: "B" Number of atoms: 2934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 184, 2934 Classifications: {'peptide': 184} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 175} Chain: "C" Number of atoms: 4514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 4514 Classifications: {'peptide': 285} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 268} Chain breaks: 2 Chain: "D" Number of atoms: 177 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 177 Classifications: {'peptide': 13} Modifications used: {'COO': 1} Link IDs: {'TRANS': 12} Time building chain proxies: 8.58, per 1000 atoms: 0.50 Number of scatterers: 17304 At special positions: 0 Unit cell: (69.01, 107.12, 167.89, 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 O 1565 8.00 N 1436 7.00 C 5544 6.00 H 8703 1.00 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=0, symmetry=0 Time building additional restraints: 4.17 Conformation dependent library (CDL) restraints added in 1.3 seconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2060 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 9 sheets defined 51.3% alpha, 20.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 116 through 128 removed outlier: 4.004A pdb=" N LYS A 120 " --> pdb=" O PRO A 116 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 201 Processing helix chain 'A' and resid 203 through 216 Processing helix chain 'A' and resid 217 through 219 No H-bonds generated for 'chain 'A' and resid 217 through 219' Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 270 through 285 Processing helix chain 'A' and resid 289 through 299 Processing helix chain 'A' and resid 300 through 302 No H-bonds generated for 'chain 'A' and resid 300 through 302' Processing helix chain 'A' and resid 303 through 308 removed outlier: 4.257A pdb=" N LEU A 307 " --> pdb=" O CYS A 303 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N SER A 308 " --> pdb=" O ASN A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 308' Processing helix chain 'A' and resid 310 through 323 Proline residue: A 317 - end of helix removed outlier: 3.609A pdb=" N ILE A 323 " --> pdb=" O LEU A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 326 No H-bonds generated for 'chain 'A' and resid 324 through 326' Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 352 through 354 No H-bonds generated for 'chain 'A' and resid 352 through 354' Processing helix chain 'A' and resid 355 through 366 removed outlier: 3.841A pdb=" N PHE A 359 " --> pdb=" O ASN A 355 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LYS A 366 " --> pdb=" O LEU A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 381 Processing helix chain 'A' and resid 383 through 388 Processing helix chain 'A' and resid 391 through 404 Processing helix chain 'A' and resid 407 through 421 removed outlier: 3.625A pdb=" N LYS A 420 " --> pdb=" O GLU A 416 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU A 421 " --> pdb=" O ARG A 417 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 435 Processing helix chain 'A' and resid 436 through 443 removed outlier: 3.771A pdb=" N THR A 442 " --> pdb=" O GLU A 438 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 443 " --> pdb=" O PHE A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 454 Processing helix chain 'A' and resid 460 through 475 removed outlier: 4.130A pdb=" N LEU A 464 " --> pdb=" O PRO A 460 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU A 474 " --> pdb=" O LEU A 470 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 480 No H-bonds generated for 'chain 'A' and resid 478 through 480' Processing helix chain 'A' and resid 481 through 494 Processing helix chain 'A' and resid 498 through 517 removed outlier: 3.627A pdb=" N ASN A 504 " --> pdb=" O GLN A 500 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N CYS A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL A 508 " --> pdb=" O ASN A 504 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N TRP A 509 " --> pdb=" O CYS A 505 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLU A 511 " --> pdb=" O GLU A 507 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TYR A 512 " --> pdb=" O VAL A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 518 through 534 Processing helix chain 'A' and resid 535 through 541 removed outlier: 5.637A pdb=" N PHE A 539 " --> pdb=" O ASP A 536 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 557 Processing helix chain 'A' and resid 559 through 566 Processing helix chain 'A' and resid 569 through 576 removed outlier: 3.754A pdb=" N PHE A 576 " --> pdb=" O PHE A 572 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 596 Processing helix chain 'A' and resid 603 through 619 Processing helix chain 'A' and resid 626 through 642 Processing helix chain 'A' and resid 650 through 664 Processing helix chain 'A' and resid 667 through 688 removed outlier: 3.620A pdb=" N LEU A 671 " --> pdb=" O LEU A 667 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 712 Processing helix chain 'A' and resid 713 through 715 No H-bonds generated for 'chain 'A' and resid 713 through 715' Processing helix chain 'A' and resid 718 through 734 Processing helix chain 'A' and resid 743 through 752 Processing helix chain 'A' and resid 753 through 755 No H-bonds generated for 'chain 'A' and resid 753 through 755' Processing helix chain 'A' and resid 769 through 784 Processing helix chain 'B' and resid 23 through 30 removed outlier: 4.023A pdb=" N LYS B 28 " --> pdb=" O ALA B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 55 removed outlier: 3.739A pdb=" N TYR B 50 " --> pdb=" O THR B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 111 Processing helix chain 'C' and resid 160 through 164 removed outlier: 3.513A pdb=" N LEU C 164 " --> pdb=" O PRO C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 169 through 173 removed outlier: 3.957A pdb=" N LEU C 172 " --> pdb=" O GLU C 169 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 59 through 62 removed outlier: 6.234A pdb=" N ILE B 38 " --> pdb=" O HIS B 61 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 76 through 81 removed outlier: 6.714A pdb=" N LEU B 115 " --> pdb=" O ILE B 134 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 4 through 9 Processing sheet with id=AA4, first strand: chain 'C' and resid 15 through 16 Processing sheet with id=AA5, first strand: chain 'C' and resid 34 through 36 Processing sheet with id=AA6, first strand: chain 'C' and resid 69 through 79 removed outlier: 8.049A pdb=" N ILE C 71 " --> pdb=" O VAL C 47 " (cutoff:3.500A) removed outlier: 9.400A pdb=" N VAL C 47 " --> pdb=" O ILE C 71 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N ASN C 73 " --> pdb=" O GLY C 45 " (cutoff:3.500A) removed outlier: 7.425A pdb=" N GLY C 45 " --> pdb=" O ASN C 73 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N THR C 75 " --> pdb=" O MET C 43 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N MET C 43 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLU C 77 " --> pdb=" O LEU C 41 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU C 41 " --> pdb=" O GLU C 77 " (cutoff:3.500A) removed outlier: 4.516A pdb=" N GLY C 38 " --> pdb=" O LYS C 125 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 155 through 159 removed outlier: 3.624A pdb=" N LEU C 182 " --> pdb=" O VAL C 155 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 180 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N LEU C 177 " --> pdb=" O GLU C 200 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU C 200 " --> pdb=" O LEU C 177 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 227 through 239 removed outlier: 6.929A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 279 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 209 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 277 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 211 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 275 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 213 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 273 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 215 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU C 271 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 217 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS C 269 " --> pdb=" O GLU C 217 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 227 through 239 removed outlier: 6.929A pdb=" N LEU C 213 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ASN C 234 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU C 211 " --> pdb=" O ASN C 234 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N GLN C 236 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL C 209 " --> pdb=" O GLN C 236 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N ALA C 238 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG C 207 " --> pdb=" O ALA C 238 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N LEU C 279 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N VAL C 209 " --> pdb=" O VAL C 277 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N VAL C 277 " --> pdb=" O VAL C 209 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N LEU C 211 " --> pdb=" O ASN C 275 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ASN C 275 " --> pdb=" O LEU C 211 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N LEU C 213 " --> pdb=" O GLU C 273 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLU C 273 " --> pdb=" O LEU C 213 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ARG C 215 " --> pdb=" O GLU C 271 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N GLU C 271 " --> pdb=" O ARG C 215 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 217 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N LYS C 269 " --> pdb=" O GLU C 217 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE C 272 " --> pdb=" O LEU C 292 " (cutoff:3.500A) 465 hydrogen bonds defined for protein. 1329 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: 6.39 Time building geometry restraints manager: 4.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8672 1.03 - 1.23: 87 1.23 - 1.43: 3537 1.43 - 1.62: 5107 1.62 - 1.82: 81 Bond restraints: 17484 Sorted by residual: bond pdb=" C ASN B 135 " pdb=" O ASN B 135 " ideal model delta sigma weight residual 1.242 1.202 0.040 1.16e-02 7.43e+03 1.19e+01 bond pdb=" N ILE C 250 " pdb=" CA ILE C 250 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.40e+00 bond pdb=" N SER C 208 " pdb=" H SER C 208 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" N LYS B 27 " pdb=" H LYS B 27 " ideal model delta sigma weight residual 0.860 0.915 -0.055 2.00e-02 2.50e+03 7.43e+00 bond pdb=" N GLU C 210 " pdb=" CA GLU C 210 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.29e-02 6.01e+03 7.43e+00 ... (remaining 17479 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 31145 1.76 - 3.51: 485 3.51 - 5.27: 60 5.27 - 7.02: 2 7.02 - 8.78: 3 Bond angle restraints: 31695 Sorted by residual: angle pdb=" N PHE C 258 " pdb=" CA PHE C 258 " pdb=" C PHE C 258 " ideal model delta sigma weight residual 112.54 103.84 8.70 1.22e+00 6.72e-01 5.09e+01 angle pdb=" N ASP D 467 " pdb=" CA ASP D 467 " pdb=" C ASP D 467 " ideal model delta sigma weight residual 111.07 106.29 4.78 1.07e+00 8.73e-01 2.00e+01 angle pdb=" CA ASP C 283 " pdb=" C ASP C 283 " pdb=" O ASP C 283 " ideal model delta sigma weight residual 121.54 117.11 4.43 1.16e+00 7.43e-01 1.46e+01 angle pdb=" N HIS A 369 " pdb=" CA HIS A 369 " pdb=" C HIS A 369 " ideal model delta sigma weight residual 113.17 108.57 4.60 1.26e+00 6.30e-01 1.33e+01 angle pdb=" CA ASN B 43 " pdb=" C ASN B 43 " pdb=" O ASN B 43 " ideal model delta sigma weight residual 121.54 117.32 4.22 1.16e+00 7.43e-01 1.32e+01 ... (remaining 31690 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 7392 17.92 - 35.85: 603 35.85 - 53.77: 164 53.77 - 71.69: 43 71.69 - 89.61: 11 Dihedral angle restraints: 8213 sinusoidal: 4460 harmonic: 3753 Sorted by residual: dihedral pdb=" CD ARG C 256 " pdb=" NE ARG C 256 " pdb=" CZ ARG C 256 " pdb=" NH1 ARG C 256 " ideal model delta sinusoidal sigma weight residual 0.00 56.89 -56.89 1 1.00e+01 1.00e-02 4.36e+01 dihedral pdb=" CA ILE B 95 " pdb=" C ILE B 95 " pdb=" N PRO B 96 " pdb=" CA PRO B 96 " ideal model delta harmonic sigma weight residual 180.00 161.89 18.11 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PRO B 136 " pdb=" C PRO B 136 " pdb=" N GLY B 137 " pdb=" CA GLY B 137 " ideal model delta harmonic sigma weight residual -180.00 -162.66 -17.34 0 5.00e+00 4.00e-02 1.20e+01 ... (remaining 8210 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 1084 0.044 - 0.089: 202 0.089 - 0.133: 77 0.133 - 0.178: 10 0.178 - 0.222: 2 Chirality restraints: 1375 Sorted by residual: chirality pdb=" CA ILE C 250 " pdb=" N ILE C 250 " pdb=" C ILE C 250 " pdb=" CB ILE C 250 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA LEU A 733 " pdb=" N LEU A 733 " pdb=" C LEU A 733 " pdb=" CB LEU A 733 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA LEU C 211 " pdb=" N LEU C 211 " pdb=" C LEU C 211 " pdb=" CB LEU C 211 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.41e-01 ... (remaining 1372 not shown) Planarity restraints: 2525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 135 " 0.055 2.00e-02 2.50e+03 4.41e-01 2.91e+03 pdb=" CG ASN B 135 " -0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN B 135 " -0.053 2.00e-02 2.50e+03 pdb=" ND2 ASN B 135 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 135 " 0.764 2.00e-02 2.50e+03 pdb="HD22 ASN B 135 " -0.759 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 43 " -0.201 2.00e-02 2.50e+03 2.32e-01 8.04e+02 pdb=" CG ASN B 43 " 0.001 2.00e-02 2.50e+03 pdb=" OD1 ASN B 43 " 0.201 2.00e-02 2.50e+03 pdb=" ND2 ASN B 43 " 0.001 2.00e-02 2.50e+03 pdb="HD21 ASN B 43 " 0.346 2.00e-02 2.50e+03 pdb="HD22 ASN B 43 " -0.348 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN D 459 " 0.166 2.00e-02 2.50e+03 1.86e-01 5.17e+02 pdb=" CG ASN D 459 " -0.005 2.00e-02 2.50e+03 pdb=" OD1 ASN D 459 " -0.164 2.00e-02 2.50e+03 pdb=" ND2 ASN D 459 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN D 459 " 0.278 2.00e-02 2.50e+03 pdb="HD22 ASN D 459 " -0.273 2.00e-02 2.50e+03 ... (remaining 2522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 1360 2.21 - 2.81: 37182 2.81 - 3.40: 47271 3.40 - 4.00: 61047 4.00 - 4.60: 94478 Nonbonded interactions: 241338 Sorted by model distance: nonbonded pdb="HH11 ARG C 11 " pdb=" O VAL C 15 " model vdw 1.612 2.450 nonbonded pdb=" H ASN A 622 " pdb=" OG1 THR A 625 " model vdw 1.612 2.450 nonbonded pdb=" O THR A 711 " pdb=" HG SER A 714 " model vdw 1.626 2.450 nonbonded pdb=" H ARG C 126 " pdb=" OD1 ASP C 132 " model vdw 1.641 2.450 nonbonded pdb=" OE1 GLN A 545 " pdb=" H GLN A 545 " model vdw 1.656 2.450 ... (remaining 241333 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: 2.080 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: 0.290 Extract box with map and model: 0.630 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 37.430 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5388 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8781 Z= 0.255 Angle : 0.656 8.781 11887 Z= 0.388 Chirality : 0.043 0.222 1375 Planarity : 0.012 0.414 1505 Dihedral : 14.952 89.613 3242 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.21 % Allowed : 9.40 % Favored : 90.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.26), residues: 1057 helix: 0.74 (0.24), residues: 485 sheet: -0.12 (0.38), residues: 186 loop : -0.43 (0.33), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 397 HIS 0.009 0.001 HIS A 618 PHE 0.036 0.002 PHE B 110 TYR 0.021 0.002 TYR A 725 ARG 0.007 0.001 ARG C 296 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 185 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.7598 (t80) cc_final: 0.7154 (t80) REVERT: A 431 VAL cc_start: 0.5136 (t) cc_final: 0.4917 (t) REVERT: A 533 MET cc_start: 0.6272 (mmm) cc_final: 0.5896 (mmm) REVERT: C 1 MET cc_start: 0.4699 (mmm) cc_final: 0.4498 (mmm) REVERT: C 10 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7059 (ttmm) REVERT: C 78 MET cc_start: 0.5682 (tpt) cc_final: 0.5469 (tpt) REVERT: C 264 GLU cc_start: 0.6777 (mp0) cc_final: 0.6566 (mp0) outliers start: 2 outliers final: 1 residues processed: 187 average time/residue: 0.5140 time to fit residues: 129.3821 Evaluate side-chains 161 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 160 time to evaluate : 1.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 286 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 0.3980 chunk 44 optimal weight: 2.9990 chunk 27 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 0.9990 chunk 61 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN C 234 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.176894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4249 r_free = 0.4249 target = 0.162153 restraints weight = 42098.194| |-----------------------------------------------------------------------------| r_work (start): 0.4246 rms_B_bonded: 2.88 r_work: 0.4140 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 8781 Z= 0.327 Angle : 0.729 10.327 11887 Z= 0.384 Chirality : 0.045 0.199 1375 Planarity : 0.007 0.099 1505 Dihedral : 5.600 89.355 1146 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.54 % Favored : 95.36 % Rotamer: Outliers : 1.96 % Allowed : 10.54 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.25), residues: 1057 helix: 0.43 (0.22), residues: 495 sheet: -0.01 (0.38), residues: 183 loop : -0.48 (0.32), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 490 HIS 0.008 0.002 HIS B 119 PHE 0.036 0.003 PHE A 361 TYR 0.017 0.002 TYR A 338 ARG 0.006 0.001 ARG A 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 185 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 307 LEU cc_start: 0.4860 (mt) cc_final: 0.4604 (mp) REVERT: A 404 TYR cc_start: 0.7886 (t80) cc_final: 0.7550 (t80) REVERT: A 405 HIS cc_start: 0.6267 (OUTLIER) cc_final: 0.5973 (t70) REVERT: A 512 TYR cc_start: 0.6094 (t80) cc_final: 0.5785 (t80) REVERT: A 533 MET cc_start: 0.6057 (mmm) cc_final: 0.5779 (mmm) REVERT: C 10 LYS cc_start: 0.7869 (ttpp) cc_final: 0.7301 (ttmm) REVERT: C 234 ASN cc_start: 0.7934 (OUTLIER) cc_final: 0.7713 (m-40) REVERT: C 285 LEU cc_start: 0.5470 (mt) cc_final: 0.5171 (mt) REVERT: D 463 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6229 (tm-30) outliers start: 19 outliers final: 9 residues processed: 190 average time/residue: 0.5004 time to fit residues: 129.2446 Evaluate side-chains 180 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 169 time to evaluate : 1.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 549 ILE Chi-restraints excluded: chain A residue 580 SER Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 52 SER Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 234 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.7980 chunk 89 optimal weight: 0.9980 chunk 64 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 46 optimal weight: 0.0980 chunk 91 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 96 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN C 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.174530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.158891 restraints weight = 41754.408| |-----------------------------------------------------------------------------| r_work (start): 0.4207 rms_B_bonded: 3.11 r_work: 0.4096 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6065 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.120 8781 Z= 0.293 Angle : 0.587 6.527 11887 Z= 0.317 Chirality : 0.041 0.167 1375 Planarity : 0.005 0.069 1505 Dihedral : 5.343 88.479 1144 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.07 % Allowed : 13.95 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.26), residues: 1057 helix: 0.81 (0.23), residues: 495 sheet: 0.05 (0.37), residues: 187 loop : -0.23 (0.33), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 PHE 0.047 0.002 PHE B 110 TYR 0.020 0.002 TYR B 73 ARG 0.006 0.001 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8117 (t80) cc_final: 0.7797 (t80) REVERT: A 405 HIS cc_start: 0.6607 (OUTLIER) cc_final: 0.6353 (t70) REVERT: A 512 TYR cc_start: 0.6542 (t80) cc_final: 0.6323 (t80) REVERT: A 528 ASP cc_start: 0.6344 (OUTLIER) cc_final: 0.5696 (t0) REVERT: A 615 LYS cc_start: 0.7974 (tmmt) cc_final: 0.7504 (tmmt) REVERT: A 721 ARG cc_start: 0.6911 (ttm170) cc_final: 0.6535 (mtm180) REVERT: C 10 LYS cc_start: 0.7881 (ttpp) cc_final: 0.7339 (ttmm) REVERT: C 196 GLU cc_start: 0.5024 (mp0) cc_final: 0.4673 (mp0) REVERT: C 258 PHE cc_start: 0.5974 (OUTLIER) cc_final: 0.3803 (m-80) REVERT: C 285 LEU cc_start: 0.5820 (OUTLIER) cc_final: 0.5515 (mt) outliers start: 20 outliers final: 10 residues processed: 195 average time/residue: 0.5053 time to fit residues: 134.2870 Evaluate side-chains 197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 183 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 405 HIS Chi-restraints excluded: chain A residue 423 ASN Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 2 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 103 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.7980 chunk 88 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 236 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.174161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.158878 restraints weight = 41866.671| |-----------------------------------------------------------------------------| r_work (start): 0.4195 rms_B_bonded: 2.97 r_work: 0.4090 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6181 moved from start: 0.5085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 8781 Z= 0.297 Angle : 0.596 5.458 11887 Z= 0.321 Chirality : 0.041 0.149 1375 Planarity : 0.005 0.067 1505 Dihedral : 5.395 88.286 1144 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.27 % Allowed : 13.74 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.26), residues: 1057 helix: 0.71 (0.23), residues: 500 sheet: 0.08 (0.38), residues: 187 loop : -0.34 (0.33), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 397 HIS 0.006 0.001 HIS A 462 PHE 0.034 0.002 PHE B 110 TYR 0.016 0.002 TYR B 73 ARG 0.006 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8139 (t80) cc_final: 0.7934 (t80) REVERT: A 528 ASP cc_start: 0.6214 (OUTLIER) cc_final: 0.5676 (t0) REVERT: A 721 ARG cc_start: 0.7072 (ttm170) cc_final: 0.6689 (ttm170) REVERT: B 97 TRP cc_start: 0.7293 (m-10) cc_final: 0.6754 (m-10) REVERT: C 10 LYS cc_start: 0.7911 (ttpp) cc_final: 0.7337 (ttmm) REVERT: C 95 PHE cc_start: 0.6029 (m-80) cc_final: 0.5639 (m-10) REVERT: C 196 GLU cc_start: 0.5225 (mp0) cc_final: 0.4815 (mp0) REVERT: C 258 PHE cc_start: 0.6267 (OUTLIER) cc_final: 0.4443 (t80) REVERT: C 285 LEU cc_start: 0.6061 (OUTLIER) cc_final: 0.5792 (mt) outliers start: 22 outliers final: 13 residues processed: 216 average time/residue: 0.4799 time to fit residues: 142.1003 Evaluate side-chains 208 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 192 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 47 LYS Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 34 optimal weight: 0.5980 chunk 19 optimal weight: 0.6980 chunk 60 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 20 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN B 17 HIS C 191 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.174864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159276 restraints weight = 41488.231| |-----------------------------------------------------------------------------| r_work (start): 0.4206 rms_B_bonded: 2.99 r_work: 0.4093 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6221 moved from start: 0.5620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8781 Z= 0.240 Angle : 0.568 5.594 11887 Z= 0.302 Chirality : 0.040 0.143 1375 Planarity : 0.005 0.067 1505 Dihedral : 5.310 89.782 1144 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.76 % Allowed : 15.60 % Favored : 82.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1057 helix: 0.93 (0.23), residues: 498 sheet: 0.13 (0.38), residues: 187 loop : -0.34 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.033 0.002 PHE B 110 TYR 0.013 0.001 TYR B 73 ARG 0.006 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 200 time to evaluate : 1.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8095 (t80) cc_final: 0.7815 (t80) REVERT: A 528 ASP cc_start: 0.6216 (OUTLIER) cc_final: 0.5729 (t0) REVERT: A 721 ARG cc_start: 0.7100 (ttm170) cc_final: 0.6678 (ttm170) REVERT: B 97 TRP cc_start: 0.7451 (m-10) cc_final: 0.6763 (m-10) REVERT: B 100 MET cc_start: 0.6649 (mtm) cc_final: 0.6341 (mtm) REVERT: B 107 GLN cc_start: 0.6817 (tm-30) cc_final: 0.6196 (tm-30) REVERT: C 10 LYS cc_start: 0.7891 (ttpp) cc_final: 0.7307 (ttmm) REVERT: C 95 PHE cc_start: 0.6037 (m-80) cc_final: 0.5647 (m-10) REVERT: C 196 GLU cc_start: 0.5244 (mp0) cc_final: 0.4810 (mp0) REVERT: C 259 THR cc_start: 0.6987 (p) cc_final: 0.6749 (p) outliers start: 17 outliers final: 12 residues processed: 207 average time/residue: 0.5084 time to fit residues: 142.4487 Evaluate side-chains 210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 28 optimal weight: 0.1980 chunk 51 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 62 optimal weight: 0.4980 chunk 41 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN C 146 GLN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.174279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4205 r_free = 0.4205 target = 0.159041 restraints weight = 41463.096| |-----------------------------------------------------------------------------| r_work (start): 0.4204 rms_B_bonded: 2.92 r_work: 0.4093 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.6110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8781 Z= 0.242 Angle : 0.567 6.291 11887 Z= 0.300 Chirality : 0.040 0.144 1375 Planarity : 0.005 0.066 1505 Dihedral : 5.280 89.540 1144 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 1.96 % Allowed : 16.63 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.26), residues: 1057 helix: 0.99 (0.23), residues: 498 sheet: 0.14 (0.38), residues: 187 loop : -0.37 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 397 HIS 0.005 0.001 HIS A 462 PHE 0.030 0.002 PHE B 110 TYR 0.014 0.001 TYR B 73 ARG 0.005 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 1.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8063 (t80) cc_final: 0.7762 (t80) REVERT: A 512 TYR cc_start: 0.6905 (t80) cc_final: 0.6608 (t80) REVERT: A 528 ASP cc_start: 0.6137 (OUTLIER) cc_final: 0.5652 (t0) REVERT: A 721 ARG cc_start: 0.7171 (ttm170) cc_final: 0.6692 (ttm170) REVERT: A 730 GLN cc_start: 0.6599 (OUTLIER) cc_final: 0.6240 (mt0) REVERT: B 97 TRP cc_start: 0.7561 (m-10) cc_final: 0.6804 (m-10) REVERT: B 107 GLN cc_start: 0.6821 (tm-30) cc_final: 0.6185 (tm-30) REVERT: B 108 ARG cc_start: 0.7547 (mmm-85) cc_final: 0.7088 (mmm-85) REVERT: C 10 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7316 (ttmm) REVERT: C 95 PHE cc_start: 0.6044 (m-80) cc_final: 0.5693 (m-10) REVERT: C 160 THR cc_start: 0.6983 (OUTLIER) cc_final: 0.6712 (p) REVERT: C 196 GLU cc_start: 0.5294 (mp0) cc_final: 0.4826 (mp0) outliers start: 19 outliers final: 11 residues processed: 209 average time/residue: 0.5248 time to fit residues: 148.4448 Evaluate side-chains 210 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 730 GLN Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain D residue 459 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 0.5980 chunk 52 optimal weight: 0.2980 chunk 32 optimal weight: 0.2980 chunk 39 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 5 optimal weight: 0.0980 chunk 70 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 94 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 overall best weight: 0.3980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 597 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 267 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.175382 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.160165 restraints weight = 41377.584| |-----------------------------------------------------------------------------| r_work (start): 0.4216 rms_B_bonded: 2.89 r_work: 0.4108 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6247 moved from start: 0.6322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8781 Z= 0.203 Angle : 0.555 6.698 11887 Z= 0.289 Chirality : 0.040 0.142 1375 Planarity : 0.005 0.065 1505 Dihedral : 5.176 88.985 1144 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.34 % Allowed : 18.18 % Favored : 80.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.26), residues: 1057 helix: 1.13 (0.23), residues: 498 sheet: 0.17 (0.38), residues: 187 loop : -0.35 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 397 HIS 0.004 0.001 HIS A 462 PHE 0.029 0.002 PHE A 361 TYR 0.010 0.001 TYR B 52 ARG 0.003 0.000 ARG B 64 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 199 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 404 TYR cc_start: 0.8089 (t80) cc_final: 0.7789 (t80) REVERT: A 512 TYR cc_start: 0.6860 (t80) cc_final: 0.6538 (t80) REVERT: A 528 ASP cc_start: 0.6012 (OUTLIER) cc_final: 0.5529 (t0) REVERT: A 721 ARG cc_start: 0.7143 (ttm170) cc_final: 0.6672 (ttm170) REVERT: B 48 GLU cc_start: 0.7242 (mp0) cc_final: 0.6644 (mp0) REVERT: B 97 TRP cc_start: 0.7683 (m-10) cc_final: 0.6971 (m-10) REVERT: B 107 GLN cc_start: 0.6826 (tm-30) cc_final: 0.6175 (tm-30) REVERT: C 10 LYS cc_start: 0.7910 (ttpp) cc_final: 0.7318 (ttmm) REVERT: C 95 PHE cc_start: 0.6032 (m-80) cc_final: 0.5694 (m-10) REVERT: C 160 THR cc_start: 0.6998 (OUTLIER) cc_final: 0.6714 (p) REVERT: C 196 GLU cc_start: 0.5264 (mp0) cc_final: 0.4738 (mp0) outliers start: 13 outliers final: 9 residues processed: 206 average time/residue: 0.5217 time to fit residues: 144.9367 Evaluate side-chains 206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 195 time to evaluate : 1.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 264 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 53 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 0.7980 chunk 80 optimal weight: 0.0970 chunk 88 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 overall best weight: 0.2778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 234 ASN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.176003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4228 r_free = 0.4228 target = 0.160844 restraints weight = 41395.100| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.89 r_work: 0.4116 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.4116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6240 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8781 Z= 0.180 Angle : 0.547 7.312 11887 Z= 0.282 Chirality : 0.040 0.142 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.044 87.621 1144 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 1.03 % Allowed : 18.70 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.26), residues: 1057 helix: 1.31 (0.23), residues: 497 sheet: 0.05 (0.37), residues: 194 loop : -0.25 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 397 HIS 0.006 0.001 HIS A 618 PHE 0.027 0.001 PHE B 110 TYR 0.009 0.001 TYR A 128 ARG 0.004 0.000 ARG A 318 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 196 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7299 (mtpt) cc_final: 0.6967 (mmtt) REVERT: A 404 TYR cc_start: 0.8095 (t80) cc_final: 0.7783 (t80) REVERT: A 512 TYR cc_start: 0.6902 (t80) cc_final: 0.6553 (t80) REVERT: A 528 ASP cc_start: 0.6010 (OUTLIER) cc_final: 0.5546 (t0) REVERT: A 721 ARG cc_start: 0.7134 (ttm170) cc_final: 0.6825 (ttm170) REVERT: B 48 GLU cc_start: 0.7207 (mp0) cc_final: 0.6624 (mp0) REVERT: B 97 TRP cc_start: 0.7690 (m-10) cc_final: 0.6973 (m-10) REVERT: C 10 LYS cc_start: 0.7908 (ttpp) cc_final: 0.7308 (ttmm) REVERT: C 95 PHE cc_start: 0.6003 (m-80) cc_final: 0.5659 (m-10) REVERT: C 160 THR cc_start: 0.7009 (OUTLIER) cc_final: 0.6740 (p) REVERT: C 196 GLU cc_start: 0.5282 (mp0) cc_final: 0.4758 (mp0) REVERT: C 231 GLU cc_start: 0.7461 (pt0) cc_final: 0.6990 (pt0) outliers start: 10 outliers final: 6 residues processed: 202 average time/residue: 0.5340 time to fit residues: 145.3845 Evaluate side-chains 199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 191 time to evaluate : 1.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 234 ASN Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 39 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 64 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 105 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 84 optimal weight: 0.9990 chunk 99 optimal weight: 0.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 191 GLN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.173786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4200 r_free = 0.4200 target = 0.158649 restraints weight = 41437.860| |-----------------------------------------------------------------------------| r_work (start): 0.4172 rms_B_bonded: 2.88 r_work: 0.4053 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.4053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.6964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8781 Z= 0.284 Angle : 0.602 7.500 11887 Z= 0.318 Chirality : 0.041 0.148 1375 Planarity : 0.005 0.072 1505 Dihedral : 5.276 89.772 1144 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.45 % Allowed : 19.11 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.26), residues: 1057 helix: 1.09 (0.23), residues: 498 sheet: -0.17 (0.37), residues: 199 loop : -0.43 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 PHE 0.024 0.002 PHE B 110 TYR 0.015 0.002 TYR B 143 ARG 0.007 0.001 ARG B 108 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 195 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7384 (mtpt) cc_final: 0.7061 (mmtt) REVERT: A 404 TYR cc_start: 0.8112 (t80) cc_final: 0.7735 (t80) REVERT: A 512 TYR cc_start: 0.7034 (t80) cc_final: 0.6676 (t80) REVERT: A 528 ASP cc_start: 0.6324 (OUTLIER) cc_final: 0.5863 (t0) REVERT: A 615 LYS cc_start: 0.8228 (tmmt) cc_final: 0.7787 (tmmt) REVERT: A 702 ARG cc_start: 0.7485 (mtt180) cc_final: 0.7280 (mpt-90) REVERT: A 721 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6845 (ttm170) REVERT: B 27 LYS cc_start: 0.5908 (mmmm) cc_final: 0.5675 (mttp) REVERT: B 46 THR cc_start: 0.6361 (OUTLIER) cc_final: 0.6073 (p) REVERT: B 48 GLU cc_start: 0.7261 (mp0) cc_final: 0.6652 (mp0) REVERT: B 107 GLN cc_start: 0.6999 (tm-30) cc_final: 0.6291 (tm-30) REVERT: C 10 LYS cc_start: 0.7931 (ttpp) cc_final: 0.7320 (ttmm) REVERT: C 160 THR cc_start: 0.7089 (OUTLIER) cc_final: 0.6796 (p) REVERT: C 196 GLU cc_start: 0.5376 (mp0) cc_final: 0.4820 (mp0) REVERT: C 231 GLU cc_start: 0.7657 (pt0) cc_final: 0.7123 (pt0) outliers start: 14 outliers final: 9 residues processed: 206 average time/residue: 0.4934 time to fit residues: 137.6302 Evaluate side-chains 201 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 189 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 57 optimal weight: 0.9990 chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 99 optimal weight: 0.6980 chunk 12 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 79 optimal weight: 0.9990 chunk 18 optimal weight: 0.7980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.172868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.157113 restraints weight = 41513.481| |-----------------------------------------------------------------------------| r_work (start): 0.4165 rms_B_bonded: 2.96 r_work: 0.4055 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.4055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6338 moved from start: 0.7408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8781 Z= 0.245 Angle : 0.586 8.763 11887 Z= 0.310 Chirality : 0.041 0.152 1375 Planarity : 0.005 0.063 1505 Dihedral : 5.198 86.391 1144 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.24 % Allowed : 20.04 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1057 helix: 1.21 (0.23), residues: 499 sheet: -0.11 (0.37), residues: 193 loop : -0.46 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 280 HIS 0.004 0.001 HIS A 462 PHE 0.029 0.002 PHE B 110 TYR 0.011 0.001 TYR B 73 ARG 0.003 0.000 ARG B 64 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 188 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7371 (mtpt) cc_final: 0.7019 (mmtt) REVERT: A 404 TYR cc_start: 0.8110 (t80) cc_final: 0.7703 (t80) REVERT: A 512 TYR cc_start: 0.7062 (t80) cc_final: 0.6577 (t80) REVERT: A 528 ASP cc_start: 0.6327 (OUTLIER) cc_final: 0.5839 (t0) REVERT: A 615 LYS cc_start: 0.8174 (tmmt) cc_final: 0.7773 (tmmt) REVERT: A 721 ARG cc_start: 0.7345 (ttm170) cc_final: 0.6898 (ttm170) REVERT: B 27 LYS cc_start: 0.5959 (mmmm) cc_final: 0.5729 (mttp) REVERT: B 46 THR cc_start: 0.6383 (OUTLIER) cc_final: 0.6118 (p) REVERT: B 48 GLU cc_start: 0.7339 (mp0) cc_final: 0.6777 (mp0) REVERT: B 79 VAL cc_start: 0.6293 (m) cc_final: 0.4749 (p) REVERT: C 10 LYS cc_start: 0.7955 (ttpp) cc_final: 0.7338 (ttmm) REVERT: C 160 THR cc_start: 0.7153 (OUTLIER) cc_final: 0.6826 (p) REVERT: C 196 GLU cc_start: 0.5312 (mp0) cc_final: 0.4714 (mp0) REVERT: C 231 GLU cc_start: 0.7533 (pt0) cc_final: 0.7005 (pt0) outliers start: 12 outliers final: 9 residues processed: 197 average time/residue: 0.5096 time to fit residues: 135.3144 Evaluate side-chains 195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 183 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 528 ASP Chi-restraints excluded: chain A residue 532 HIS Chi-restraints excluded: chain A residue 534 THR Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain C residue 50 GLN Chi-restraints excluded: chain C residue 107 GLU Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 269 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 10 optimal weight: 0.9990 chunk 104 optimal weight: 0.7980 chunk 96 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 20 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 HIS C 191 GLN C 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.171249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155611 restraints weight = 41460.993| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 2.94 r_work: 0.4038 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6388 moved from start: 0.7699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8781 Z= 0.288 Angle : 0.607 9.634 11887 Z= 0.320 Chirality : 0.042 0.144 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.337 87.581 1144 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.30 % Favored : 94.61 % Rotamer: Outliers : 1.45 % Allowed : 20.45 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.26), residues: 1057 helix: 1.19 (0.23), residues: 500 sheet: -0.17 (0.36), residues: 213 loop : -0.58 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 PHE 0.026 0.002 PHE B 110 TYR 0.012 0.002 TYR B 143 ARG 0.005 0.001 ARG B 64 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7679.50 seconds wall clock time: 136 minutes 4.34 seconds (8164.34 seconds total)