Starting phenix.real_space_refine on Fri Aug 22 18:54:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.cif Found real_map, /net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.map" model { file = "/net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8toh_41452/08_2025/8toh_41452.cif" } resolution = 3.29 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= 0.002 sd= 0.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 4554 2.51 5 N 1199 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7022 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 860, 7022 Classifications: {'peptide': 860} Link IDs: {'PTRANS': 49, 'TRANS': 810} Chain breaks: 2 Time building chain proxies: 1.63, per 1000 atoms: 0.23 Number of scatterers: 7022 At special positions: 0 Unit cell: (72.8784, 76.1319, 115.825, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 1244 8.00 N 1199 7.00 C 4554 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.52 Conformation dependent library (CDL) restraints added in 369.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1600 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 8 sheets defined 47.1% alpha, 9.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 36 through 38 No H-bonds generated for 'chain 'A' and resid 36 through 38' Processing helix chain 'A' and resid 39 through 45 removed outlier: 4.317A pdb=" N ALA A 43 " --> pdb=" O ALA A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 56 Processing helix chain 'A' and resid 72 through 77 removed outlier: 3.598A pdb=" N THR A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 85 Processing helix chain 'A' and resid 88 through 96 removed outlier: 3.866A pdb=" N THR A 92 " --> pdb=" O SER A 88 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N HIS A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N HIS A 96 " --> pdb=" O THR A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 125 removed outlier: 3.774A pdb=" N VAL A 124 " --> pdb=" O THR A 121 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ALA A 125 " --> pdb=" O GLY A 122 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 121 through 125' Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.750A pdb=" N THR A 136 " --> pdb=" O VAL A 132 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ALA A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 166 through 184 Processing helix chain 'A' and resid 198 through 203 removed outlier: 4.187A pdb=" N ALA A 203 " --> pdb=" O ARG A 199 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 209 removed outlier: 4.245A pdb=" N ALA A 208 " --> pdb=" O GLY A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 210 through 228 removed outlier: 4.011A pdb=" N ASP A 214 " --> pdb=" O ARG A 210 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ARG A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR A 219 " --> pdb=" O HIS A 215 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA A 220 " --> pdb=" O PHE A 216 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N PHE A 224 " --> pdb=" O ALA A 220 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ARG A 225 " --> pdb=" O GLU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 249 removed outlier: 3.541A pdb=" N HIS A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLY A 247 " --> pdb=" O VAL A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 260 through 286 removed outlier: 3.962A pdb=" N GLY A 264 " --> pdb=" O SER A 260 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N LEU A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N THR A 284 " --> pdb=" O HIS A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 290 Processing helix chain 'A' and resid 309 through 324 removed outlier: 3.552A pdb=" N VAL A 323 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 333 Proline residue: A 330 - end of helix removed outlier: 3.639A pdb=" N ILE A 333 " --> pdb=" O LYS A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.502A pdb=" N LYS A 342 " --> pdb=" O PRO A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 361 removed outlier: 3.666A pdb=" N LYS A 358 " --> pdb=" O GLU A 354 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.558A pdb=" N PHE A 386 " --> pdb=" O HIS A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 394 through 405 removed outlier: 3.578A pdb=" N SER A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N TRP A 400 " --> pdb=" O GLN A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 448 removed outlier: 3.918A pdb=" N TYR A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 442 " --> pdb=" O ILE A 438 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 470 No H-bonds generated for 'chain 'A' and resid 468 through 470' Processing helix chain 'A' and resid 491 through 502 removed outlier: 3.879A pdb=" N ILE A 501 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 502 " --> pdb=" O GLN A 498 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 589 removed outlier: 4.360A pdb=" N GLN A 581 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 587 " --> pdb=" O ALA A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 598 through 603 Processing helix chain 'A' and resid 612 through 629 removed outlier: 3.844A pdb=" N LEU A 616 " --> pdb=" O ASN A 612 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR A 619 " --> pdb=" O ILE A 615 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 620 " --> pdb=" O LEU A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 678 removed outlier: 3.584A pdb=" N TYR A 669 " --> pdb=" O ALA A 665 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N GLU A 676 " --> pdb=" O LEU A 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 696 through 718 removed outlier: 3.964A pdb=" N ASN A 702 " --> pdb=" O SER A 698 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA A 708 " --> pdb=" O LEU A 704 " (cutoff:3.500A) Processing helix chain 'A' and resid 742 through 757 removed outlier: 3.721A pdb=" N LYS A 746 " --> pdb=" O SER A 742 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLU A 750 " --> pdb=" O LYS A 746 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ARG A 751 " --> pdb=" O GLU A 747 " (cutoff:3.500A) Processing helix chain 'A' and resid 771 through 781 Processing helix chain 'A' and resid 790 through 798 removed outlier: 3.759A pdb=" N LYS A 795 " --> pdb=" O GLU A 791 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU A 796 " --> pdb=" O ASP A 792 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN A 798 " --> pdb=" O LYS A 794 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 864 removed outlier: 3.555A pdb=" N LYS A 854 " --> pdb=" O TRP A 850 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 855 " --> pdb=" O GLY A 851 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LYS A 860 " --> pdb=" O LEU A 856 " (cutoff:3.500A) Processing helix chain 'A' and resid 884 through 904 removed outlier: 3.699A pdb=" N TYR A 889 " --> pdb=" O GLN A 885 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N GLN A 892 " --> pdb=" O VAL A 888 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ALA A 901 " --> pdb=" O GLU A 897 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS A 902 " --> pdb=" O ALA A 898 " (cutoff:3.500A) Processing helix chain 'A' and resid 939 through 951 removed outlier: 3.652A pdb=" N HIS A 943 " --> pdb=" O ALA A 939 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ILE A 947 " --> pdb=" O HIS A 943 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69 removed outlier: 7.840A pdb=" N ILE A 410 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N TYR A 455 " --> pdb=" O ILE A 410 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE A 412 " --> pdb=" O TYR A 455 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ALA A 457 " --> pdb=" O ILE A 412 " (cutoff:3.500A) removed outlier: 7.156A pdb=" N GLU A 414 " --> pdb=" O ALA A 457 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU A 369 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N PHE A 366 " --> pdb=" O VAL A 294 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N ILE A 296 " --> pdb=" O PHE A 366 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N TRP A 234 " --> pdb=" O SER A 295 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ALA A 297 " --> pdb=" O TRP A 234 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N THR A 236 " --> pdb=" O ALA A 297 " (cutoff:3.500A) removed outlier: 12.037A pdb=" N SER A 299 " --> pdb=" O THR A 236 " (cutoff:3.500A) removed outlier: 10.423A pdb=" N ASP A 238 " --> pdb=" O SER A 299 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N ILE A 235 " --> pdb=" O PRO A 187 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N VAL A 189 " --> pdb=" O ILE A 235 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N ILE A 237 " --> pdb=" O VAL A 189 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TYR A 147 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N THR A 190 " --> pdb=" O TYR A 147 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N PHE A 149 " --> pdb=" O THR A 190 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 304 removed outlier: 4.048A pdb=" N TRP A 302 " --> pdb=" O SER A 391 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER A 391 " --> pdb=" O TRP A 302 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N LEU A 389 " --> pdb=" O ASN A 304 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420 Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 595 removed outlier: 5.807A pdb=" N VAL A 527 " --> pdb=" O ARG A 594 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 634 through 635 removed outlier: 5.701A pdb=" N VAL A 635 " --> pdb=" O ILE A 685 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N MET A 687 " --> pdb=" O VAL A 635 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N TRP A 684 " --> pdb=" O SER A 727 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N ALA A 729 " --> pdb=" O TRP A 684 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N THR A 686 " --> pdb=" O ALA A 729 " (cutoff:3.500A) removed outlier: 11.642A pdb=" N GLN A 731 " --> pdb=" O THR A 686 " (cutoff:3.500A) removed outlier: 11.204A pdb=" N ASN A 688 " --> pdb=" O GLN A 731 " (cutoff:3.500A) removed outlier: 9.200A pdb=" N ALA A 805 " --> pdb=" O ILE A 726 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N ILE A 728 " --> pdb=" O ALA A 805 " (cutoff:3.500A) removed outlier: 7.783A pdb=" N SER A 807 " --> pdb=" O ILE A 728 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N LEU A 730 " --> pdb=" O SER A 807 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU A 804 " --> pdb=" O TYR A 869 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ILE A 871 " --> pdb=" O LEU A 804 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N LEU A 806 " --> pdb=" O ILE A 871 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 737 removed outlier: 3.503A pdb=" N GLU A 736 " --> pdb=" O ILE A 812 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL A 814 " --> pdb=" O GLU A 736 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 824 through 825 Processing sheet with id=AA8, first strand: chain 'A' and resid 928 through 931 removed outlier: 3.605A pdb=" N ARG A 929 " --> pdb=" O GLU A 936 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU A 936 " --> pdb=" O ARG A 929 " (cutoff:3.500A) 228 hydrogen bonds defined for protein. 657 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: 0.86 Time building geometry restraints manager: 0.76 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2248 1.34 - 1.46: 1791 1.46 - 1.58: 3168 1.58 - 1.69: 0 1.69 - 1.81: 42 Bond restraints: 7249 Sorted by residual: bond pdb=" C TRP A 638 " pdb=" N GLN A 639 " ideal model delta sigma weight residual 1.329 1.358 -0.029 1.35e-02 5.49e+03 4.65e+00 bond pdb=" CB PRO A 35 " pdb=" CG PRO A 35 " ideal model delta sigma weight residual 1.492 1.573 -0.081 5.00e-02 4.00e+02 2.62e+00 bond pdb=" C ALA A 254 " pdb=" N PRO A 255 " ideal model delta sigma weight residual 1.328 1.346 -0.018 1.25e-02 6.40e+03 2.10e+00 bond pdb=" CB LYS A 329 " pdb=" CG LYS A 329 " ideal model delta sigma weight residual 1.520 1.555 -0.035 3.00e-02 1.11e+03 1.34e+00 bond pdb=" CB GLN A 230 " pdb=" CG GLN A 230 " ideal model delta sigma weight residual 1.520 1.553 -0.033 3.00e-02 1.11e+03 1.22e+00 ... (remaining 7244 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 9572 1.52 - 3.04: 253 3.04 - 4.57: 24 4.57 - 6.09: 8 6.09 - 7.61: 5 Bond angle restraints: 9862 Sorted by residual: angle pdb=" N VAL A 132 " pdb=" CA VAL A 132 " pdb=" C VAL A 132 " ideal model delta sigma weight residual 113.47 109.22 4.25 1.01e+00 9.80e-01 1.77e+01 angle pdb=" CB LYS A 329 " pdb=" CG LYS A 329 " pdb=" CD LYS A 329 " ideal model delta sigma weight residual 111.30 118.91 -7.61 2.30e+00 1.89e-01 1.10e+01 angle pdb=" CA LYS A 329 " pdb=" CB LYS A 329 " pdb=" CG LYS A 329 " ideal model delta sigma weight residual 114.10 120.54 -6.44 2.00e+00 2.50e-01 1.04e+01 angle pdb=" CA GLN A 230 " pdb=" CB GLN A 230 " pdb=" CG GLN A 230 " ideal model delta sigma weight residual 114.10 119.61 -5.51 2.00e+00 2.50e-01 7.60e+00 angle pdb=" CA GLN A 731 " pdb=" CB GLN A 731 " pdb=" CG GLN A 731 " ideal model delta sigma weight residual 114.10 119.58 -5.48 2.00e+00 2.50e-01 7.50e+00 ... (remaining 9857 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.19: 3649 15.19 - 30.37: 402 30.37 - 45.55: 115 45.55 - 60.74: 23 60.74 - 75.92: 7 Dihedral angle restraints: 4196 sinusoidal: 1695 harmonic: 2501 Sorted by residual: dihedral pdb=" CA HIS A 880 " pdb=" C HIS A 880 " pdb=" N ALA A 881 " pdb=" CA ALA A 881 " ideal model delta harmonic sigma weight residual 180.00 159.30 20.70 0 5.00e+00 4.00e-02 1.71e+01 dihedral pdb=" CA THR A 632 " pdb=" C THR A 632 " pdb=" N PRO A 633 " pdb=" CA PRO A 633 " ideal model delta harmonic sigma weight residual -180.00 -161.49 -18.51 0 5.00e+00 4.00e-02 1.37e+01 dihedral pdb=" CA ILE A 438 " pdb=" C ILE A 438 " pdb=" N MET A 439 " pdb=" CA MET A 439 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 ... (remaining 4193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 590 0.029 - 0.057: 267 0.057 - 0.086: 97 0.086 - 0.115: 48 0.115 - 0.143: 9 Chirality restraints: 1011 Sorted by residual: chirality pdb=" CA ILE A 870 " pdb=" N ILE A 870 " pdb=" C ILE A 870 " pdb=" CB ILE A 870 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.12e-01 chirality pdb=" CA ILE A 685 " pdb=" N ILE A 685 " pdb=" C ILE A 685 " pdb=" CB ILE A 685 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.48e-01 chirality pdb=" CA TRP A 279 " pdb=" N TRP A 279 " pdb=" C TRP A 279 " pdb=" CB TRP A 279 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.34e-01 ... (remaining 1008 not shown) Planarity restraints: 1273 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 279 " -0.031 2.00e-02 2.50e+03 2.30e-02 1.32e+01 pdb=" CG TRP A 279 " 0.061 2.00e-02 2.50e+03 pdb=" CD1 TRP A 279 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP A 279 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 279 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A 279 " -0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP A 279 " 0.005 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 279 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 279 " -0.009 2.00e-02 2.50e+03 pdb=" CH2 TRP A 279 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 689 " 0.039 5.00e-02 4.00e+02 5.93e-02 5.63e+00 pdb=" N PRO A 690 " -0.103 5.00e-02 4.00e+02 pdb=" CA PRO A 690 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 690 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 260 " -0.026 5.00e-02 4.00e+02 3.97e-02 2.53e+00 pdb=" N PRO A 261 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO A 261 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 261 " -0.022 5.00e-02 4.00e+02 ... (remaining 1270 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1209 2.76 - 3.30: 7073 3.30 - 3.83: 12180 3.83 - 4.37: 14197 4.37 - 4.90: 23515 Nonbonded interactions: 58174 Sorted by model distance: nonbonded pdb=" OD1 ASN A 873 " pdb=" OH TYR A 912 " model vdw 2.227 3.040 nonbonded pdb=" O SER A 596 " pdb=" OH TYR A 619 " model vdw 2.228 3.040 nonbonded pdb=" NH2 ARG A 148 " pdb=" OD2 ASP A 238 " model vdw 2.241 3.120 nonbonded pdb=" NH2 ARG A 134 " pdb=" O ASP A 485 " model vdw 2.244 3.120 nonbonded pdb=" OG1 THR A 92 " pdb=" NE2 GLN A 198 " model vdw 2.255 3.120 ... (remaining 58169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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: 2.660 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: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6433 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 : 0.003 0.081 7249 Z= 0.118 Angle : 0.582 7.611 9862 Z= 0.317 Chirality : 0.041 0.143 1011 Planarity : 0.004 0.059 1273 Dihedral : 14.462 75.924 2596 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 13.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.67 (0.28), residues: 854 helix: -0.54 (0.29), residues: 316 sheet: -0.66 (0.59), residues: 85 loop : -1.61 (0.29), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 671 TYR 0.011 0.001 TYR A 531 PHE 0.016 0.001 PHE A 332 TRP 0.061 0.002 TRP A 279 HIS 0.006 0.001 HIS A 146 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 7249) covalent geometry : angle 0.58209 ( 9862) hydrogen bonds : bond 0.31200 ( 228) hydrogen bonds : angle 10.20215 ( 657) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 0.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6379 (pt0) REVERT: A 262 ARG cc_start: 0.7336 (tmt-80) cc_final: 0.7117 (tpt90) REVERT: A 266 LEU cc_start: 0.8012 (tp) cc_final: 0.7564 (tp) REVERT: A 386 PHE cc_start: 0.7884 (m-80) cc_final: 0.7608 (m-80) REVERT: A 502 GLU cc_start: 0.7071 (mp0) cc_final: 0.6867 (mp0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.0667 time to fit residues: 12.0744 Evaluate side-chains 127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 127 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.1980 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.0670 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.4980 overall best weight: 0.4118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 396 GLN A 608 GLN A 902 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.201133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179754 restraints weight = 11143.225| |-----------------------------------------------------------------------------| r_work (start): 0.4322 rms_B_bonded: 3.70 r_work: 0.4190 rms_B_bonded: 4.43 restraints_weight: 0.5000 r_work (final): 0.4190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6438 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7249 Z= 0.128 Angle : 0.595 6.363 9862 Z= 0.307 Chirality : 0.044 0.169 1011 Planarity : 0.005 0.039 1273 Dihedral : 4.784 22.829 946 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 0.82 % Allowed : 10.37 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.22 (0.28), residues: 854 helix: 0.14 (0.28), residues: 332 sheet: -0.24 (0.59), residues: 87 loop : -1.71 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 671 TYR 0.017 0.001 TYR A 531 PHE 0.016 0.001 PHE A 861 TRP 0.017 0.002 TRP A 279 HIS 0.012 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 7249) covalent geometry : angle 0.59458 ( 9862) hydrogen bonds : bond 0.04851 ( 228) hydrogen bonds : angle 6.06434 ( 657) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 142 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8024 (m-70) cc_final: 0.7792 (m170) REVERT: A 234 TRP cc_start: 0.5941 (m100) cc_final: 0.4100 (m100) REVERT: A 262 ARG cc_start: 0.7442 (tmt-80) cc_final: 0.7209 (tmt-80) REVERT: A 360 ILE cc_start: 0.7658 (tt) cc_final: 0.7287 (tt) REVERT: A 386 PHE cc_start: 0.7896 (m-80) cc_final: 0.7591 (m-80) REVERT: A 439 MET cc_start: 0.7141 (mmp) cc_final: 0.6518 (mmp) REVERT: A 502 GLU cc_start: 0.7512 (mp0) cc_final: 0.7059 (mp0) REVERT: A 744 LYS cc_start: 0.8547 (tptp) cc_final: 0.8343 (tptm) REVERT: A 815 ASP cc_start: 0.6171 (t0) cc_final: 0.5969 (t0) REVERT: A 946 LYS cc_start: 0.7559 (mmmm) cc_final: 0.7349 (mtpp) outliers start: 6 outliers final: 4 residues processed: 145 average time/residue: 0.0698 time to fit residues: 13.5886 Evaluate side-chains 139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 135 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 0.2980 chunk 80 optimal weight: 0.7980 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 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 198 GLN ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.197254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4287 r_free = 0.4287 target = 0.176108 restraints weight = 11120.525| |-----------------------------------------------------------------------------| r_work (start): 0.4297 rms_B_bonded: 3.66 r_work: 0.4163 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7249 Z= 0.136 Angle : 0.562 7.474 9862 Z= 0.292 Chirality : 0.043 0.161 1011 Planarity : 0.005 0.056 1273 Dihedral : 4.809 22.268 946 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 1.77 % Allowed : 14.32 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.29), residues: 854 helix: 0.41 (0.29), residues: 331 sheet: -0.40 (0.57), residues: 89 loop : -1.70 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 148 TYR 0.017 0.002 TYR A 531 PHE 0.020 0.001 PHE A 861 TRP 0.018 0.001 TRP A 850 HIS 0.013 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 7249) covalent geometry : angle 0.56193 ( 9862) hydrogen bonds : bond 0.04394 ( 228) hydrogen bonds : angle 5.55183 ( 657) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 133 time to evaluate : 0.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7564 (tpp-160) cc_final: 0.7297 (tpp-160) REVERT: A 52 GLU cc_start: 0.6918 (mt-10) cc_final: 0.6252 (mt-10) REVERT: A 234 TRP cc_start: 0.6166 (m100) cc_final: 0.4474 (m100) REVERT: A 262 ARG cc_start: 0.7534 (tmt-80) cc_final: 0.7137 (tmt-80) REVERT: A 415 ASN cc_start: 0.8486 (t0) cc_final: 0.8268 (t0) REVERT: A 436 LYS cc_start: 0.8172 (tptp) cc_final: 0.7844 (tptp) REVERT: A 744 LYS cc_start: 0.8490 (tptp) cc_final: 0.8288 (tptm) REVERT: A 803 PHE cc_start: 0.6708 (p90) cc_final: 0.5971 (p90) REVERT: A 946 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7382 (mtpp) outliers start: 13 outliers final: 9 residues processed: 137 average time/residue: 0.0728 time to fit residues: 13.5471 Evaluate side-chains 143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 134 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 747 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 26 optimal weight: 0.6980 chunk 49 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.0770 chunk 8 optimal weight: 0.6980 chunk 73 optimal weight: 0.0670 chunk 13 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN A 283 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.198124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.176941 restraints weight = 11233.449| |-----------------------------------------------------------------------------| r_work (start): 0.4309 rms_B_bonded: 3.68 r_work: 0.4176 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6463 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 7249 Z= 0.109 Angle : 0.543 7.201 9862 Z= 0.281 Chirality : 0.042 0.163 1011 Planarity : 0.004 0.046 1273 Dihedral : 4.649 22.078 946 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 3.14 % Allowed : 14.46 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.93 (0.29), residues: 854 helix: 0.59 (0.30), residues: 330 sheet: 0.02 (0.62), residues: 79 loop : -1.73 (0.29), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.015 0.001 TYR A 531 PHE 0.022 0.001 PHE A 861 TRP 0.018 0.001 TRP A 850 HIS 0.013 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 7249) covalent geometry : angle 0.54281 ( 9862) hydrogen bonds : bond 0.03687 ( 228) hydrogen bonds : angle 5.21600 ( 657) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 137 time to evaluate : 0.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7961 (m-70) cc_final: 0.7735 (m170) REVERT: A 230 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6767 (pt0) REVERT: A 234 TRP cc_start: 0.6223 (m100) cc_final: 0.4354 (m100) REVERT: A 262 ARG cc_start: 0.7402 (tmt-80) cc_final: 0.7045 (tmt-80) REVERT: A 397 LEU cc_start: 0.7789 (OUTLIER) cc_final: 0.7564 (tt) REVERT: A 404 GLU cc_start: 0.7983 (tp30) cc_final: 0.7534 (tp30) REVERT: A 431 MET cc_start: 0.7421 (ttp) cc_final: 0.7200 (ttm) REVERT: A 436 LYS cc_start: 0.8000 (tptp) cc_final: 0.7718 (tptp) REVERT: A 502 GLU cc_start: 0.7535 (mp0) cc_final: 0.7060 (mp0) REVERT: A 744 LYS cc_start: 0.8421 (tptp) cc_final: 0.8209 (tptm) REVERT: A 900 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7835 (mtpp) REVERT: A 925 PHE cc_start: 0.5999 (OUTLIER) cc_final: 0.5768 (m-80) REVERT: A 946 LYS cc_start: 0.7495 (mmmm) cc_final: 0.7284 (ttmm) outliers start: 23 outliers final: 12 residues processed: 149 average time/residue: 0.0814 time to fit residues: 16.5413 Evaluate side-chains 143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 129 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 12 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 23 optimal weight: 0.0870 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 61 optimal weight: 3.9990 overall best weight: 0.7160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 GLN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 283 ASN A 902 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.197830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176602 restraints weight = 11031.637| |-----------------------------------------------------------------------------| r_work (start): 0.4289 rms_B_bonded: 3.67 r_work: 0.4154 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4154 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6524 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7249 Z= 0.139 Angle : 0.576 6.909 9862 Z= 0.300 Chirality : 0.043 0.158 1011 Planarity : 0.004 0.047 1273 Dihedral : 4.752 21.801 946 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.73 % Allowed : 15.28 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.06 (0.29), residues: 854 helix: 0.57 (0.30), residues: 331 sheet: -0.79 (0.55), residues: 94 loop : -1.73 (0.29), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.020 0.002 TYR A 863 PHE 0.022 0.001 PHE A 861 TRP 0.021 0.001 TRP A 850 HIS 0.014 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7249) covalent geometry : angle 0.57582 ( 9862) hydrogen bonds : bond 0.03875 ( 228) hydrogen bonds : angle 5.19439 ( 657) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7632 (tpp-160) cc_final: 0.7362 (tpp-160) REVERT: A 52 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6015 (pt0) REVERT: A 95 HIS cc_start: 0.8025 (m-70) cc_final: 0.7818 (m170) REVERT: A 234 TRP cc_start: 0.6164 (m100) cc_final: 0.4063 (m100) REVERT: A 262 ARG cc_start: 0.7480 (tmt-80) cc_final: 0.7024 (tmt-80) REVERT: A 397 LEU cc_start: 0.7925 (OUTLIER) cc_final: 0.7641 (tt) REVERT: A 404 GLU cc_start: 0.7984 (tp30) cc_final: 0.7522 (tp30) REVERT: A 436 LYS cc_start: 0.8045 (tptp) cc_final: 0.7758 (tptp) REVERT: A 450 VAL cc_start: 0.8147 (OUTLIER) cc_final: 0.7512 (t) REVERT: A 622 MET cc_start: 0.6719 (ppp) cc_final: 0.6429 (ppp) REVERT: A 744 LYS cc_start: 0.8445 (tptp) cc_final: 0.8220 (tptm) REVERT: A 803 PHE cc_start: 0.6776 (p90) cc_final: 0.6074 (p90) REVERT: A 863 TYR cc_start: 0.6701 (m-10) cc_final: 0.6386 (m-10) REVERT: A 900 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7861 (mtpp) REVERT: A 925 PHE cc_start: 0.6280 (OUTLIER) cc_final: 0.6043 (m-80) REVERT: A 946 LYS cc_start: 0.7585 (mmmm) cc_final: 0.7366 (ttmm) outliers start: 20 outliers final: 13 residues processed: 148 average time/residue: 0.0835 time to fit residues: 16.7409 Evaluate side-chains 149 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 283 ASN Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 588 MET Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 70 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 76 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 840 ASN A 902 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.198008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.176337 restraints weight = 11113.576| |-----------------------------------------------------------------------------| r_work (start): 0.4283 rms_B_bonded: 3.72 r_work: 0.4144 rms_B_bonded: 4.50 restraints_weight: 0.5000 r_work (final): 0.4144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6539 moved from start: 0.2700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7249 Z= 0.139 Angle : 0.578 6.997 9862 Z= 0.299 Chirality : 0.043 0.167 1011 Planarity : 0.004 0.050 1273 Dihedral : 4.770 21.956 946 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 3.27 % Allowed : 15.83 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.09 (0.29), residues: 854 helix: 0.55 (0.29), residues: 332 sheet: -0.73 (0.55), residues: 92 loop : -1.78 (0.29), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.017 0.002 TYR A 531 PHE 0.022 0.001 PHE A 861 TRP 0.023 0.001 TRP A 850 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 7249) covalent geometry : angle 0.57846 ( 9862) hydrogen bonds : bond 0.03766 ( 228) hydrogen bonds : angle 5.12514 ( 657) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 133 time to evaluate : 0.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7676 (tpp-160) cc_final: 0.7403 (tpp-160) REVERT: A 52 GLU cc_start: 0.6936 (mt-10) cc_final: 0.5853 (pt0) REVERT: A 230 GLN cc_start: 0.7095 (tm-30) cc_final: 0.6735 (pt0) REVERT: A 234 TRP cc_start: 0.6215 (m100) cc_final: 0.4074 (m100) REVERT: A 262 ARG cc_start: 0.7501 (tmt-80) cc_final: 0.6996 (tpt90) REVERT: A 397 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7642 (tt) REVERT: A 404 GLU cc_start: 0.7958 (tp30) cc_final: 0.7484 (tp30) REVERT: A 436 LYS cc_start: 0.8048 (tptp) cc_final: 0.7740 (tptp) REVERT: A 450 VAL cc_start: 0.8192 (OUTLIER) cc_final: 0.7552 (t) REVERT: A 744 LYS cc_start: 0.8452 (tptp) cc_final: 0.8216 (tptm) REVERT: A 803 PHE cc_start: 0.6780 (p90) cc_final: 0.6086 (p90) REVERT: A 900 LYS cc_start: 0.8102 (mtpp) cc_final: 0.7848 (mtpp) REVERT: A 925 PHE cc_start: 0.6326 (OUTLIER) cc_final: 0.6080 (m-80) REVERT: A 946 LYS cc_start: 0.7570 (mmmm) cc_final: 0.7348 (ttmm) outliers start: 24 outliers final: 12 residues processed: 145 average time/residue: 0.0739 time to fit residues: 14.7984 Evaluate side-chains 147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 73 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 54 optimal weight: 0.0770 chunk 66 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 388 GLN A 844 GLN A 902 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.198087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.176438 restraints weight = 11067.006| |-----------------------------------------------------------------------------| r_work (start): 0.4299 rms_B_bonded: 3.72 r_work: 0.4168 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6498 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7249 Z= 0.117 Angle : 0.578 9.755 9862 Z= 0.294 Chirality : 0.043 0.160 1011 Planarity : 0.004 0.050 1273 Dihedral : 4.705 21.892 946 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 3.00 % Allowed : 16.23 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.04 (0.29), residues: 854 helix: 0.62 (0.30), residues: 331 sheet: -0.66 (0.58), residues: 89 loop : -1.79 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.017 0.001 TYR A 531 PHE 0.022 0.001 PHE A 861 TRP 0.023 0.001 TRP A 850 HIS 0.008 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00265 ( 7249) covalent geometry : angle 0.57776 ( 9862) hydrogen bonds : bond 0.03464 ( 228) hydrogen bonds : angle 5.01233 ( 657) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 138 time to evaluate : 0.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7685 (tpp-160) cc_final: 0.7419 (tpp-160) REVERT: A 52 GLU cc_start: 0.6930 (mt-10) cc_final: 0.5803 (pt0) REVERT: A 234 TRP cc_start: 0.6173 (m100) cc_final: 0.4122 (m100) REVERT: A 262 ARG cc_start: 0.7478 (tmt-80) cc_final: 0.6985 (tpt90) REVERT: A 397 LEU cc_start: 0.7875 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 404 GLU cc_start: 0.7969 (tp30) cc_final: 0.7469 (tp30) REVERT: A 436 LYS cc_start: 0.8021 (tptp) cc_final: 0.7731 (tptp) REVERT: A 744 LYS cc_start: 0.8441 (tptp) cc_final: 0.8240 (tptm) REVERT: A 803 PHE cc_start: 0.6776 (p90) cc_final: 0.6074 (p90) REVERT: A 900 LYS cc_start: 0.8069 (mtpp) cc_final: 0.7810 (mtpp) REVERT: A 925 PHE cc_start: 0.6286 (OUTLIER) cc_final: 0.6067 (m-10) REVERT: A 946 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7352 (ttmm) outliers start: 22 outliers final: 14 residues processed: 149 average time/residue: 0.0818 time to fit residues: 16.4983 Evaluate side-chains 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 730 LEU Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 7 optimal weight: 0.0970 chunk 57 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 55 optimal weight: 4.9990 chunk 27 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 84 optimal weight: 4.9990 chunk 20 optimal weight: 0.0670 chunk 21 optimal weight: 0.7980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.199055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.177035 restraints weight = 11329.340| |-----------------------------------------------------------------------------| r_work (start): 0.4295 rms_B_bonded: 3.78 r_work: 0.4161 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.4161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7249 Z= 0.119 Angle : 0.597 11.493 9862 Z= 0.302 Chirality : 0.043 0.159 1011 Planarity : 0.004 0.049 1273 Dihedral : 4.693 21.828 946 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 2.59 % Allowed : 16.64 % Favored : 80.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.02 (0.29), residues: 854 helix: 0.66 (0.30), residues: 329 sheet: -0.92 (0.54), residues: 99 loop : -1.74 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 387 TYR 0.018 0.001 TYR A 531 PHE 0.023 0.001 PHE A 861 TRP 0.025 0.001 TRP A 850 HIS 0.013 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7249) covalent geometry : angle 0.59693 ( 9862) hydrogen bonds : bond 0.03409 ( 228) hydrogen bonds : angle 5.00837 ( 657) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 136 time to evaluate : 0.153 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7379 (tpp-160) REVERT: A 52 GLU cc_start: 0.6924 (mt-10) cc_final: 0.5746 (pt0) REVERT: A 81 GLN cc_start: 0.7412 (pm20) cc_final: 0.7035 (mp10) REVERT: A 230 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6578 (pt0) REVERT: A 234 TRP cc_start: 0.6157 (m100) cc_final: 0.4162 (m100) REVERT: A 262 ARG cc_start: 0.7505 (tmt-80) cc_final: 0.6995 (tpt90) REVERT: A 397 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7561 (tt) REVERT: A 404 GLU cc_start: 0.7988 (tp30) cc_final: 0.7542 (tp30) REVERT: A 431 MET cc_start: 0.7431 (ttp) cc_final: 0.7162 (ttm) REVERT: A 436 LYS cc_start: 0.7975 (tptp) cc_final: 0.7667 (tptp) REVERT: A 450 VAL cc_start: 0.8184 (OUTLIER) cc_final: 0.7919 (m) REVERT: A 803 PHE cc_start: 0.6786 (p90) cc_final: 0.6106 (p90) REVERT: A 900 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7792 (mtpp) REVERT: A 925 PHE cc_start: 0.6274 (OUTLIER) cc_final: 0.6039 (m-80) REVERT: A 946 LYS cc_start: 0.7576 (mmmm) cc_final: 0.7352 (ttmm) outliers start: 19 outliers final: 12 residues processed: 147 average time/residue: 0.0793 time to fit residues: 15.9474 Evaluate side-chains 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 20 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 5 optimal weight: 0.0570 chunk 68 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 3 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.199679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.178144 restraints weight = 11054.119| |-----------------------------------------------------------------------------| r_work (start): 0.4302 rms_B_bonded: 3.75 r_work: 0.4164 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.4164 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6491 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7249 Z= 0.114 Angle : 0.586 11.316 9862 Z= 0.296 Chirality : 0.043 0.156 1011 Planarity : 0.004 0.049 1273 Dihedral : 4.660 21.437 946 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.32 % Allowed : 17.60 % Favored : 80.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.03 (0.29), residues: 854 helix: 0.61 (0.30), residues: 332 sheet: -0.88 (0.55), residues: 99 loop : -1.73 (0.29), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 887 TYR 0.018 0.001 TYR A 531 PHE 0.024 0.001 PHE A 861 TRP 0.026 0.001 TRP A 850 HIS 0.007 0.001 HIS A 275 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 7249) covalent geometry : angle 0.58622 ( 9862) hydrogen bonds : bond 0.03316 ( 228) hydrogen bonds : angle 4.95265 ( 657) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.254 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7691 (tpp-160) cc_final: 0.7418 (tpp-160) REVERT: A 52 GLU cc_start: 0.6920 (mt-10) cc_final: 0.5841 (pt0) REVERT: A 81 GLN cc_start: 0.7375 (pm20) cc_final: 0.6989 (mp10) REVERT: A 230 GLN cc_start: 0.7037 (tm-30) cc_final: 0.6716 (pt0) REVERT: A 234 TRP cc_start: 0.6119 (m100) cc_final: 0.4153 (m100) REVERT: A 262 ARG cc_start: 0.7516 (tmt-80) cc_final: 0.7041 (tmt-80) REVERT: A 397 LEU cc_start: 0.7876 (OUTLIER) cc_final: 0.7607 (tt) REVERT: A 404 GLU cc_start: 0.7970 (tp30) cc_final: 0.7504 (tp30) REVERT: A 431 MET cc_start: 0.7488 (ttp) cc_final: 0.7202 (ttm) REVERT: A 436 LYS cc_start: 0.7931 (tptp) cc_final: 0.7607 (tptp) REVERT: A 450 VAL cc_start: 0.8153 (OUTLIER) cc_final: 0.7485 (t) REVERT: A 645 GLN cc_start: 0.7631 (mt0) cc_final: 0.7339 (mt0) REVERT: A 744 LYS cc_start: 0.8434 (tptm) cc_final: 0.8187 (tppt) REVERT: A 803 PHE cc_start: 0.6789 (p90) cc_final: 0.6095 (p90) REVERT: A 900 LYS cc_start: 0.8043 (mtpp) cc_final: 0.7785 (mtpp) REVERT: A 925 PHE cc_start: 0.6268 (OUTLIER) cc_final: 0.6027 (m-80) REVERT: A 946 LYS cc_start: 0.7585 (mmmm) cc_final: 0.7358 (ttmm) outliers start: 17 outliers final: 12 residues processed: 144 average time/residue: 0.0828 time to fit residues: 16.3453 Evaluate side-chains 147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 132 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 886 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 0 optimal weight: 5.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 1.9990 chunk 53 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 HIS ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.194028 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4240 r_free = 0.4240 target = 0.172342 restraints weight = 11029.274| |-----------------------------------------------------------------------------| r_work (start): 0.4239 rms_B_bonded: 3.73 r_work: 0.4101 rms_B_bonded: 4.46 restraints_weight: 0.5000 r_work (final): 0.4101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6622 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7249 Z= 0.215 Angle : 0.690 12.071 9862 Z= 0.352 Chirality : 0.047 0.169 1011 Planarity : 0.005 0.050 1273 Dihedral : 5.219 21.804 946 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 16.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.43 % Favored : 91.57 % Rotamer: Outliers : 2.32 % Allowed : 17.87 % Favored : 79.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.27 (0.29), residues: 854 helix: 0.36 (0.29), residues: 333 sheet: -0.76 (0.54), residues: 100 loop : -1.90 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 887 TYR 0.024 0.002 TYR A 531 PHE 0.025 0.002 PHE A 861 TRP 0.032 0.002 TRP A 850 HIS 0.011 0.002 HIS A 902 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 7249) covalent geometry : angle 0.69007 ( 9862) hydrogen bonds : bond 0.04337 ( 228) hydrogen bonds : angle 5.30372 ( 657) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1708 Ramachandran restraints generated. 854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 131 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7772 (tpp-160) cc_final: 0.7493 (tpp-160) REVERT: A 230 GLN cc_start: 0.7120 (tm-30) cc_final: 0.6777 (pt0) REVERT: A 234 TRP cc_start: 0.6341 (m100) cc_final: 0.4272 (m100) REVERT: A 262 ARG cc_start: 0.7596 (tmt-80) cc_final: 0.6984 (tpt90) REVERT: A 404 GLU cc_start: 0.7934 (tp30) cc_final: 0.7456 (tp30) REVERT: A 431 MET cc_start: 0.7710 (ttp) cc_final: 0.7391 (ttm) REVERT: A 436 LYS cc_start: 0.8098 (tptp) cc_final: 0.7777 (tptp) REVERT: A 450 VAL cc_start: 0.8317 (OUTLIER) cc_final: 0.8037 (m) REVERT: A 502 GLU cc_start: 0.7613 (mp0) cc_final: 0.7324 (mp0) REVERT: A 645 GLN cc_start: 0.7693 (mt0) cc_final: 0.7387 (mt0) REVERT: A 900 LYS cc_start: 0.8143 (mtpp) cc_final: 0.7885 (mtpp) REVERT: A 925 PHE cc_start: 0.6648 (OUTLIER) cc_final: 0.6340 (m-80) REVERT: A 946 LYS cc_start: 0.7678 (mmmm) cc_final: 0.7450 (ttmm) outliers start: 17 outliers final: 11 residues processed: 140 average time/residue: 0.0809 time to fit residues: 15.6097 Evaluate side-chains 143 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 0.267 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 294 VAL Chi-restraints excluded: chain A residue 371 PHE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 882 GLU Chi-restraints excluded: chain A residue 899 LEU Chi-restraints excluded: chain A residue 925 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 17 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 6 optimal weight: 0.0470 chunk 69 optimal weight: 0.0050 chunk 35 optimal weight: 0.5980 chunk 85 optimal weight: 0.6980 chunk 45 optimal weight: 0.0050 chunk 36 optimal weight: 1.9990 chunk 79 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 overall best weight: 0.2106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 239 ASN A 270 ASN ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 722 GLN A 902 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.201042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4316 r_free = 0.4316 target = 0.179118 restraints weight = 11097.306| |-----------------------------------------------------------------------------| r_work (start): 0.4314 rms_B_bonded: 3.80 r_work: 0.4176 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.4176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7249 Z= 0.111 Angle : 0.613 11.863 9862 Z= 0.312 Chirality : 0.043 0.159 1011 Planarity : 0.004 0.046 1273 Dihedral : 4.748 22.058 946 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 1.36 % Allowed : 19.24 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -1.07 (0.29), residues: 854 helix: 0.53 (0.30), residues: 334 sheet: -0.41 (0.55), residues: 100 loop : -1.86 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 148 TYR 0.015 0.001 TYR A 531 PHE 0.026 0.001 PHE A 861 TRP 0.037 0.002 TRP A 279 HIS 0.009 0.001 HIS A 95 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 7249) covalent geometry : angle 0.61343 ( 9862) hydrogen bonds : bond 0.03281 ( 228) hydrogen bonds : angle 5.04034 ( 657) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1695.35 seconds wall clock time: 29 minutes 49.03 seconds (1789.03 seconds total)