Starting phenix.real_space_refine on Thu Sep 18 14:05:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9au7_43872/09_2025/9au7_43872.cif Found real_map, /net/cci-nas-00/data/ceres_data/9au7_43872/09_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_43872/09_2025/9au7_43872.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9au7_43872/09_2025/9au7_43872.map" model { file = "/net/cci-nas-00/data/ceres_data/9au7_43872/09_2025/9au7_43872.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9au7_43872/09_2025/9au7_43872.cif" } resolution = 3.4 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= 0.001 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 2.47, per 1000 atoms: 0.14 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: 1.11 Conformation dependent library (CDL) restraints added in 416.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.45 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: 4.19 Time building geometry restraints manager: 1.63 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: 2.830 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: 0.070 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.460 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- 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= 0.210 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 : 13.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.001 ARG C 296 TYR 0.021 0.002 TYR A 725 PHE 0.036 0.002 PHE B 110 TRP 0.010 0.001 TRP A 397 HIS 0.009 0.001 HIS A 618 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 8781) covalent geometry : angle 0.65616 (11887) hydrogen bonds : bond 0.12077 ( 459) hydrogen bonds : angle 6.30245 ( 1329) *********************** 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 : 0.303 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: 0.5897 (mmm) REVERT: C 1 MET cc_start: 0.4699 (mmm) cc_final: 0.4497 (mmm) REVERT: C 10 LYS cc_start: 0.7597 (ttpp) cc_final: 0.7060 (ttmm) REVERT: C 78 MET cc_start: 0.5682 (tpt) cc_final: 0.5470 (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: 0.2122 time to fit residues: 53.7843 Evaluate side-chains 162 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 161 time to evaluate : 0.286 ------------------------------------------------------------------------------- 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 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 597 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.174952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.160470 restraints weight = 41963.696| |-----------------------------------------------------------------------------| r_work (start): 0.4226 rms_B_bonded: 2.84 r_work: 0.4121 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.4121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6005 moved from start: 0.3461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 8781 Z= 0.268 Angle : 0.770 8.913 11887 Z= 0.413 Chirality : 0.047 0.191 1375 Planarity : 0.007 0.097 1505 Dihedral : 5.776 87.139 1146 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.39 % Favored : 94.51 % Rotamer: Outliers : 2.07 % Allowed : 11.36 % Favored : 86.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: -0.35 (0.25), residues: 1057 helix: 0.17 (0.22), residues: 488 sheet: -0.06 (0.38), residues: 183 loop : -0.65 (0.32), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 64 TYR 0.020 0.003 TYR B 169 PHE 0.038 0.003 PHE A 361 TRP 0.017 0.003 TRP A 199 HIS 0.010 0.002 HIS C 110 Details of bonding type rmsd covalent geometry : bond 0.00607 ( 8781) covalent geometry : angle 0.77042 (11887) hydrogen bonds : bond 0.04952 ( 459) hydrogen bonds : angle 5.64565 ( 1329) *********************** 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 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 189 time to evaluate : 0.453 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: A 404 TYR cc_start: 0.7989 (t80) cc_final: 0.7656 (t80) REVERT: A 405 HIS cc_start: 0.6400 (OUTLIER) cc_final: 0.6138 (t70) REVERT: A 512 TYR cc_start: 0.6398 (t80) cc_final: 0.6111 (t80) REVERT: A 533 MET cc_start: 0.6241 (mmm) cc_final: 0.5955 (mmm) REVERT: A 721 ARG cc_start: 0.6773 (ttm170) cc_final: 0.6410 (mtm180) REVERT: B 147 GLU cc_start: 0.6215 (mm-30) cc_final: 0.5968 (mm-30) REVERT: C 10 LYS cc_start: 0.7883 (ttpp) cc_final: 0.7316 (ttmm) REVERT: C 231 GLU cc_start: 0.7255 (pt0) cc_final: 0.6998 (pt0) REVERT: C 285 LEU cc_start: 0.5621 (mt) cc_final: 0.5271 (mt) REVERT: D 463 GLU cc_start: 0.6473 (tm-30) cc_final: 0.6195 (tm-30) outliers start: 20 outliers final: 8 residues processed: 196 average time/residue: 0.2195 time to fit residues: 58.5056 Evaluate side-chains 183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 174 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.3980 chunk 13 optimal weight: 1.9990 chunk 72 optimal weight: 0.9990 chunk 68 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 17 HIS C 191 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.173605 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4197 r_free = 0.4197 target = 0.158412 restraints weight = 42220.543| |-----------------------------------------------------------------------------| r_work (start): 0.4202 rms_B_bonded: 2.95 r_work: 0.4096 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 8781 Z= 0.202 Angle : 0.603 6.160 11887 Z= 0.325 Chirality : 0.042 0.149 1375 Planarity : 0.005 0.070 1505 Dihedral : 5.503 87.901 1144 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.86 % Allowed : 14.57 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: 0.09 (0.26), residues: 1057 helix: 0.54 (0.23), residues: 494 sheet: 0.09 (0.38), residues: 185 loop : -0.41 (0.33), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 64 TYR 0.016 0.002 TYR B 73 PHE 0.046 0.002 PHE B 110 TRP 0.007 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00459 ( 8781) covalent geometry : angle 0.60263 (11887) hydrogen bonds : bond 0.04447 ( 459) hydrogen bonds : angle 5.33348 ( 1329) *********************** 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: 18 poor density : 188 time to evaluate : 0.296 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.7108 (mtpt) cc_final: 0.6855 (mmtt) REVERT: A 364 THR cc_start: 0.6725 (OUTLIER) cc_final: 0.6483 (t) REVERT: A 404 TYR cc_start: 0.8166 (t80) cc_final: 0.7928 (t80) REVERT: A 405 HIS cc_start: 0.6595 (OUTLIER) cc_final: 0.6393 (t70) REVERT: A 512 TYR cc_start: 0.6669 (t80) cc_final: 0.6460 (t80) REVERT: A 528 ASP cc_start: 0.6219 (OUTLIER) cc_final: 0.5655 (t0) REVERT: A 615 LYS cc_start: 0.8029 (tmmt) cc_final: 0.7577 (tmmt) REVERT: A 721 ARG cc_start: 0.6946 (ttm170) cc_final: 0.6557 (mtm180) REVERT: C 10 LYS cc_start: 0.7880 (ttpp) cc_final: 0.7324 (ttmm) REVERT: C 95 PHE cc_start: 0.5946 (m-80) cc_final: 0.5588 (m-10) REVERT: C 196 GLU cc_start: 0.5076 (mp0) cc_final: 0.4713 (mp0) REVERT: C 231 GLU cc_start: 0.7553 (pt0) cc_final: 0.7320 (pt0) REVERT: C 258 PHE cc_start: 0.6151 (OUTLIER) cc_final: 0.3774 (m-80) REVERT: C 259 THR cc_start: 0.7071 (p) cc_final: 0.6844 (p) REVERT: C 285 LEU cc_start: 0.5933 (OUTLIER) cc_final: 0.5653 (mt) outliers start: 18 outliers final: 10 residues processed: 198 average time/residue: 0.2049 time to fit residues: 55.1431 Evaluate side-chains 194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 179 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 405 HIS 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 185 THR 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 41 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 104 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 87 optimal weight: 0.9990 chunk 103 optimal weight: 0.3980 chunk 93 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 100 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.174753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159522 restraints weight = 41520.359| |-----------------------------------------------------------------------------| r_work (start): 0.4205 rms_B_bonded: 2.88 r_work: 0.4098 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.4098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6222 moved from start: 0.5560 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= 0.183 Angle : 0.605 6.455 11887 Z= 0.320 Chirality : 0.041 0.146 1375 Planarity : 0.005 0.068 1505 Dihedral : 5.374 86.975 1144 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 2.38 % Allowed : 13.84 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: 0.19 (0.26), residues: 1057 helix: 0.68 (0.23), residues: 499 sheet: -0.01 (0.38), residues: 187 loop : -0.38 (0.33), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 64 TYR 0.018 0.002 TYR B 73 PHE 0.033 0.002 PHE B 110 TRP 0.026 0.002 TRP A 397 HIS 0.006 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8781) covalent geometry : angle 0.60536 (11887) hydrogen bonds : bond 0.04081 ( 459) hydrogen bonds : angle 5.13121 ( 1329) *********************** 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 224 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 201 time to evaluate : 0.350 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: A 404 TYR cc_start: 0.8143 (t80) cc_final: 0.7913 (t80) REVERT: A 528 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5644 (t0) REVERT: A 721 ARG cc_start: 0.7041 (ttm170) cc_final: 0.6588 (ttm170) REVERT: B 97 TRP cc_start: 0.7449 (m-10) cc_final: 0.6793 (m-10) REVERT: B 147 GLU cc_start: 0.6229 (mm-30) cc_final: 0.5972 (mm-30) REVERT: C 10 LYS cc_start: 0.7873 (ttpp) cc_final: 0.7276 (ttmm) REVERT: C 196 GLU cc_start: 0.5205 (mp0) cc_final: 0.4870 (mp0) REVERT: C 231 GLU cc_start: 0.7602 (pt0) cc_final: 0.7250 (pt0) REVERT: C 259 THR cc_start: 0.7047 (p) cc_final: 0.6809 (p) outliers start: 23 outliers final: 11 residues processed: 215 average time/residue: 0.2100 time to fit residues: 61.3258 Evaluate side-chains 211 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 199 time to evaluate : 0.354 ------------------------------------------------------------------------------- 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 611 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 7 ILE Chi-restraints excluded: chain C residue 69 ILE Chi-restraints excluded: chain C residue 132 ASP Chi-restraints excluded: chain C residue 190 THR Chi-restraints excluded: chain C residue 208 SER Chi-restraints excluded: chain C residue 258 PHE Chi-restraints excluded: chain C residue 265 THR 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 55 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 65 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 54 optimal weight: 0.2980 chunk 21 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 1 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 13 optimal weight: 0.8980 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 423 ASN A 597 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.174221 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.159287 restraints weight = 41337.050| |-----------------------------------------------------------------------------| r_work (start): 0.4197 rms_B_bonded: 2.86 r_work: 0.4089 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.4089 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6251 moved from start: 0.6027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8781 Z= 0.162 Angle : 0.571 6.223 11887 Z= 0.302 Chirality : 0.041 0.145 1375 Planarity : 0.005 0.067 1505 Dihedral : 5.312 89.435 1144 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.15 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.33 (0.26), residues: 1057 helix: 0.88 (0.23), residues: 498 sheet: 0.04 (0.38), residues: 187 loop : -0.43 (0.33), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 64 TYR 0.013 0.001 TYR B 73 PHE 0.029 0.002 PHE B 110 TRP 0.010 0.001 TRP A 397 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00361 ( 8781) covalent geometry : angle 0.57096 (11887) hydrogen bonds : bond 0.03992 ( 459) hydrogen bonds : angle 5.02386 ( 1329) *********************** 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 : 0.486 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 209 LYS cc_start: 0.7278 (mtpt) cc_final: 0.6953 (mmtt) REVERT: A 404 TYR cc_start: 0.8157 (t80) cc_final: 0.7892 (t80) REVERT: A 528 ASP cc_start: 0.6186 (OUTLIER) cc_final: 0.5684 (t0) REVERT: A 721 ARG cc_start: 0.7139 (ttm170) cc_final: 0.6681 (ttm170) REVERT: B 48 GLU cc_start: 0.7226 (mp0) cc_final: 0.6613 (mp0) REVERT: B 79 VAL cc_start: 0.5924 (m) cc_final: 0.5603 (m) REVERT: B 97 TRP cc_start: 0.7568 (m-10) cc_final: 0.6786 (m-10) REVERT: B 100 MET cc_start: 0.6686 (mtm) cc_final: 0.6382 (mtm) REVERT: B 147 GLU cc_start: 0.6290 (mm-30) cc_final: 0.6065 (mm-30) REVERT: C 10 LYS cc_start: 0.7877 (ttpp) cc_final: 0.7288 (ttmm) REVERT: C 196 GLU cc_start: 0.5293 (mp0) cc_final: 0.4935 (mp0) REVERT: C 231 GLU cc_start: 0.7584 (pt0) cc_final: 0.6974 (pt0) REVERT: C 259 THR cc_start: 0.7012 (p) cc_final: 0.6722 (p) outliers start: 17 outliers final: 13 residues processed: 208 average time/residue: 0.2265 time to fit residues: 62.9507 Evaluate side-chains 212 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 198 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR 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 534 THR Chi-restraints excluded: chain A residue 597 GLN Chi-restraints excluded: chain A residue 641 ILE 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 107 GLU 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 75 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.1980 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 89 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 367 GLN ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 597 GLN ** B 121 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 191 GLN C 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.172896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.157583 restraints weight = 41718.896| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 2.92 r_work: 0.4046 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4046 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6324 moved from start: 0.6506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 8781 Z= 0.206 Angle : 0.600 6.586 11887 Z= 0.321 Chirality : 0.041 0.148 1375 Planarity : 0.005 0.065 1505 Dihedral : 5.394 88.456 1144 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 2.38 % Allowed : 17.05 % Favored : 80.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: 0.13 (0.26), residues: 1057 helix: 0.70 (0.23), residues: 499 sheet: 0.08 (0.38), residues: 187 loop : -0.58 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 686 TYR 0.012 0.002 TYR B 73 PHE 0.025 0.002 PHE B 110 TRP 0.007 0.002 TRP A 397 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00460 ( 8781) covalent geometry : angle 0.59983 (11887) hydrogen bonds : bond 0.04216 ( 459) hydrogen bonds : angle 5.16470 ( 1329) *********************** 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 215 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 192 time to evaluate : 0.397 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: A 404 TYR cc_start: 0.8193 (t80) cc_final: 0.7852 (t80) REVERT: A 512 TYR cc_start: 0.7002 (t80) cc_final: 0.6714 (t80) REVERT: A 528 ASP cc_start: 0.6152 (OUTLIER) cc_final: 0.5642 (t0) REVERT: A 721 ARG cc_start: 0.7226 (ttm170) cc_final: 0.6791 (ttm170) REVERT: B 48 GLU cc_start: 0.7247 (mp0) cc_final: 0.6643 (mp0) REVERT: B 79 VAL cc_start: 0.6160 (m) cc_final: 0.5827 (m) REVERT: B 147 GLU cc_start: 0.6413 (mm-30) cc_final: 0.6202 (mm-30) REVERT: C 10 LYS cc_start: 0.7905 (ttpp) cc_final: 0.7302 (ttmm) REVERT: C 196 GLU cc_start: 0.5399 (mp0) cc_final: 0.4887 (mp0) REVERT: C 231 GLU cc_start: 0.7673 (pt0) cc_final: 0.6999 (pt0) REVERT: C 259 THR cc_start: 0.7055 (p) cc_final: 0.6772 (p) outliers start: 23 outliers final: 17 residues processed: 208 average time/residue: 0.2364 time to fit residues: 66.0539 Evaluate side-chains 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 191 time to evaluate : 0.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 364 THR Chi-restraints excluded: chain A residue 405 HIS 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 47 LYS 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 160 THR Chi-restraints excluded: chain C residue 208 SER 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 84 optimal weight: 0.8980 chunk 78 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 45 optimal weight: 0.4980 chunk 11 optimal weight: 0.9980 chunk 105 optimal weight: 0.5980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 423 ASN ** A 532 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN B 121 HIS C 191 GLN C 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.169872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4153 r_free = 0.4153 target = 0.154261 restraints weight = 41564.326| |-----------------------------------------------------------------------------| r_work (start): 0.4156 rms_B_bonded: 2.91 r_work: 0.4039 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.4039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.7084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 8781 Z= 0.203 Angle : 0.610 7.407 11887 Z= 0.326 Chirality : 0.042 0.147 1375 Planarity : 0.005 0.074 1505 Dihedral : 5.488 89.454 1144 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer: Outliers : 1.96 % Allowed : 18.08 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: 0.11 (0.26), residues: 1057 helix: 0.70 (0.23), residues: 501 sheet: 0.06 (0.38), residues: 187 loop : -0.62 (0.32), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 686 TYR 0.016 0.002 TYR B 73 PHE 0.026 0.002 PHE B 110 TRP 0.007 0.002 TRP A 280 HIS 0.005 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 8781) covalent geometry : angle 0.60974 (11887) hydrogen bonds : bond 0.04201 ( 459) hydrogen bonds : angle 5.14289 ( 1329) *********************** 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 216 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 197 time to evaluate : 0.406 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: A 241 PHE cc_start: 0.6699 (t80) cc_final: 0.6471 (t80) REVERT: A 404 TYR cc_start: 0.8190 (t80) cc_final: 0.7840 (t80) REVERT: A 495 LYS cc_start: 0.7922 (mttt) cc_final: 0.7616 (mtmm) REVERT: A 512 TYR cc_start: 0.7036 (t80) cc_final: 0.6600 (t80) REVERT: A 528 ASP cc_start: 0.6288 (OUTLIER) cc_final: 0.5814 (t0) REVERT: A 615 LYS cc_start: 0.8269 (tmmt) cc_final: 0.7800 (tmmt) REVERT: B 15 ILE cc_start: 0.6967 (mp) cc_final: 0.6749 (mm) REVERT: B 48 GLU cc_start: 0.7263 (mp0) cc_final: 0.6695 (mp0) REVERT: C 10 LYS cc_start: 0.7928 (ttpp) cc_final: 0.7308 (ttmm) REVERT: C 196 GLU cc_start: 0.5423 (mp0) cc_final: 0.4833 (mp0) REVERT: C 231 GLU cc_start: 0.7627 (pt0) cc_final: 0.6965 (pt0) REVERT: C 259 THR cc_start: 0.7066 (p) cc_final: 0.6739 (p) outliers start: 19 outliers final: 14 residues processed: 212 average time/residue: 0.2349 time to fit residues: 66.8687 Evaluate side-chains 207 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 192 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 423 ASN 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 5 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 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 78 optimal weight: 0.0770 chunk 19 optimal weight: 0.9980 chunk 96 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 80 optimal weight: 0.3980 chunk 28 optimal weight: 0.9980 chunk 42 optimal weight: 0.2980 overall best weight: 0.4738 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.173152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.157861 restraints weight = 41643.779| |-----------------------------------------------------------------------------| r_work (start): 0.4170 rms_B_bonded: 2.90 r_work: 0.4052 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.4052 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6346 moved from start: 0.7170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8781 Z= 0.151 Angle : 0.579 7.905 11887 Z= 0.305 Chirality : 0.040 0.146 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.339 87.801 1144 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 1.65 % Allowed : 18.90 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.26), residues: 1057 helix: 0.82 (0.23), residues: 502 sheet: 0.04 (0.38), residues: 187 loop : -0.60 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 64 TYR 0.011 0.001 TYR B 73 PHE 0.049 0.002 PHE B 110 TRP 0.007 0.001 TRP A 397 HIS 0.004 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 8781) covalent geometry : angle 0.57906 (11887) hydrogen bonds : bond 0.03929 ( 459) hydrogen bonds : angle 4.99060 ( 1329) *********************** 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 209 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 193 time to evaluate : 0.300 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 404 TYR cc_start: 0.8177 (t80) cc_final: 0.7794 (t80) REVERT: A 495 LYS cc_start: 0.7924 (mttt) cc_final: 0.7616 (mtmm) REVERT: A 512 TYR cc_start: 0.6992 (t80) cc_final: 0.6536 (t80) REVERT: A 528 ASP cc_start: 0.6251 (OUTLIER) cc_final: 0.5773 (t0) REVERT: A 615 LYS cc_start: 0.8252 (tmmt) cc_final: 0.7796 (tmmt) REVERT: A 715 LEU cc_start: 0.5199 (OUTLIER) cc_final: 0.4460 (mt) REVERT: A 721 ARG cc_start: 0.7294 (ttm170) cc_final: 0.6850 (ttm170) REVERT: B 15 ILE cc_start: 0.6974 (mp) cc_final: 0.6757 (mm) REVERT: B 48 GLU cc_start: 0.7266 (mp0) cc_final: 0.6684 (mp0) REVERT: C 10 LYS cc_start: 0.7919 (ttpp) cc_final: 0.7294 (ttmm) REVERT: C 160 THR cc_start: 0.7061 (OUTLIER) cc_final: 0.6758 (p) REVERT: C 196 GLU cc_start: 0.5405 (mp0) cc_final: 0.4823 (mp0) REVERT: C 231 GLU cc_start: 0.7651 (pt0) cc_final: 0.6971 (pt0) outliers start: 16 outliers final: 10 residues processed: 205 average time/residue: 0.2514 time to fit residues: 69.0411 Evaluate side-chains 200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 187 time to evaluate : 0.364 ------------------------------------------------------------------------------- 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 715 LEU Chi-restraints excluded: chain A residue 784 LEU Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 7 ILE 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 0.7980 chunk 37 optimal weight: 0.9980 chunk 7 optimal weight: 0.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 72 ASN 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 = 0.4344 r_free = 0.4344 target = 0.172962 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.156436 restraints weight = 41014.354| |-----------------------------------------------------------------------------| r_work (start): 0.4123 rms_B_bonded: 2.98 r_work: 0.4003 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.4003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6460 moved from start: 0.7788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 8781 Z= 0.270 Angle : 0.679 7.971 11887 Z= 0.367 Chirality : 0.044 0.166 1375 Planarity : 0.006 0.063 1505 Dihedral : 5.746 89.775 1144 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 2.27 % Allowed : 19.11 % Favored : 78.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: -0.31 (0.25), residues: 1057 helix: 0.40 (0.23), residues: 501 sheet: 0.01 (0.38), residues: 185 loop : -1.02 (0.32), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 417 TYR 0.021 0.002 TYR B 143 PHE 0.043 0.003 PHE B 110 TRP 0.007 0.002 TRP A 280 HIS 0.007 0.001 HIS A 727 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 8781) covalent geometry : angle 0.67910 (11887) hydrogen bonds : bond 0.04778 ( 459) hydrogen bonds : angle 5.48588 ( 1329) *********************** 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 215 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 193 time to evaluate : 0.461 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: A 404 TYR cc_start: 0.8186 (t80) cc_final: 0.7722 (t80) REVERT: A 495 LYS cc_start: 0.8045 (mttt) cc_final: 0.7770 (mttp) REVERT: A 528 ASP cc_start: 0.6230 (OUTLIER) cc_final: 0.5848 (t70) REVERT: A 615 LYS cc_start: 0.8328 (tmmt) cc_final: 0.7915 (tmmt) REVERT: B 97 TRP cc_start: 0.7813 (m-10) cc_final: 0.7418 (m-10) REVERT: C 10 LYS cc_start: 0.7921 (ttpp) cc_final: 0.7244 (ttmm) REVERT: C 160 THR cc_start: 0.7227 (OUTLIER) cc_final: 0.6862 (p) REVERT: C 196 GLU cc_start: 0.5401 (mp0) cc_final: 0.5044 (mp0) REVERT: C 231 GLU cc_start: 0.7736 (pt0) cc_final: 0.7344 (pt0) outliers start: 22 outliers final: 15 residues processed: 206 average time/residue: 0.2282 time to fit residues: 63.4643 Evaluate side-chains 203 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 186 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 202 ASP Chi-restraints excluded: chain A residue 364 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 47 LYS Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain C residue 5 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 132 ASP Chi-restraints excluded: chain C residue 160 THR Chi-restraints excluded: chain C residue 208 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 29 optimal weight: 0.9990 chunk 2 optimal weight: 0.8980 chunk 56 optimal weight: 0.1980 chunk 5 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 6 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 89 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 612 HIS C 267 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.171337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.155741 restraints weight = 41482.646| |-----------------------------------------------------------------------------| r_work (start): 0.4152 rms_B_bonded: 2.91 r_work: 0.4041 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6405 moved from start: 0.7896 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= 0.158 Angle : 0.600 9.618 11887 Z= 0.316 Chirality : 0.042 0.149 1375 Planarity : 0.005 0.063 1505 Dihedral : 5.410 84.077 1144 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 1.34 % Allowed : 20.25 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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 aren not related in a simple way. whole: 0.07 (0.26), residues: 1057 helix: 0.83 (0.23), residues: 500 sheet: -0.12 (0.37), residues: 205 loop : -0.85 (0.33), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 64 TYR 0.010 0.001 TYR B 183 PHE 0.044 0.002 PHE B 110 TRP 0.009 0.001 TRP A 397 HIS 0.004 0.001 HIS A 462 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 8781) covalent geometry : angle 0.59954 (11887) hydrogen bonds : bond 0.04043 ( 459) hydrogen bonds : angle 5.13534 ( 1329) ********************** 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 197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.485 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: A 209 LYS cc_start: 0.7384 (mtpt) cc_final: 0.7044 (mmtt) REVERT: A 322 MET cc_start: 0.6179 (mtp) cc_final: 0.5796 (mtp) REVERT: A 404 TYR cc_start: 0.8125 (t80) cc_final: 0.7662 (t80) REVERT: A 465 PHE cc_start: 0.4005 (OUTLIER) cc_final: 0.3700 (m-80) REVERT: A 495 LYS cc_start: 0.7889 (mttt) cc_final: 0.7592 (mtmm) REVERT: A 528 ASP cc_start: 0.5973 (OUTLIER) cc_final: 0.5628 (t0) REVERT: A 615 LYS cc_start: 0.8305 (tmmt) cc_final: 0.7909 (tmmt) REVERT: A 629 GLU cc_start: 0.5744 (tp30) cc_final: 0.5208 (tp30) REVERT: B 48 GLU cc_start: 0.7183 (mp0) cc_final: 0.6364 (mp0) REVERT: B 79 VAL cc_start: 0.6489 (m) cc_final: 0.4894 (p) REVERT: B 97 TRP cc_start: 0.7878 (m-10) cc_final: 0.7545 (m-10) REVERT: C 196 GLU cc_start: 0.5325 (mp0) cc_final: 0.5069 (mp0) REVERT: C 231 GLU cc_start: 0.7593 (pt0) cc_final: 0.6950 (pt0) outliers start: 13 outliers final: 10 residues processed: 193 average time/residue: 0.2525 time to fit residues: 64.9820 Evaluate side-chains 194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 182 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 THR Chi-restraints excluded: chain A residue 465 PHE 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 5 LEU Chi-restraints excluded: chain C residue 7 ILE 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 91 optimal weight: 0.8980 chunk 74 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 95 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 84 optimal weight: 0.9980 chunk 104 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.168346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.152762 restraints weight = 41377.189| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 2.90 r_work: 0.4013 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.4013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6442 moved from start: 0.8138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 8781 Z= 0.208 Angle : 0.635 10.526 11887 Z= 0.337 Chirality : 0.042 0.143 1375 Planarity : 0.005 0.064 1505 Dihedral : 5.516 86.370 1144 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 13.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.65 % Allowed : 20.25 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.02 (0.26), residues: 1057 helix: 0.80 (0.23), residues: 500 sheet: -0.08 (0.37), residues: 205 loop : -0.94 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 318 TYR 0.013 0.002 TYR B 143 PHE 0.041 0.002 PHE B 110 TRP 0.007 0.002 TRP A 397 HIS 0.012 0.001 HIS A 612 Details of bonding type rmsd covalent geometry : bond 0.00471 ( 8781) covalent geometry : angle 0.63511 (11887) hydrogen bonds : bond 0.04271 ( 459) hydrogen bonds : angle 5.23823 ( 1329) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3785.95 seconds wall clock time: 65 minutes 2.94 seconds (3902.94 seconds total)