Starting phenix.real_space_refine on Thu Nov 14 18:32:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_41452.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_41452.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_41452.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_41452.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8toh_41452/11_2024/8toh_41452.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: 4.61, per 1000 atoms: 0.66 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: 1.72 Conformation dependent library (CDL) restraints added in 983.4 milliseconds 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: 0.72 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: 2.09 Time building geometry restraints manager: 2.03 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 19.520 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.280 ------------------------------------------------------------------------------- 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= 0.160 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.061 0.002 TRP A 279 HIS 0.006 0.001 HIS A 146 PHE 0.016 0.001 PHE A 332 TYR 0.011 0.001 TYR A 531 ARG 0.003 0.000 ARG A 671 *********************** 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 : 0.783 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: 0.1903 time to fit residues: 33.8227 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 : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 43 optimal weight: 0.1980 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6503 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7249 Z= 0.222 Angle : 0.614 7.142 9862 Z= 0.319 Chirality : 0.045 0.168 1011 Planarity : 0.005 0.040 1273 Dihedral : 4.878 22.706 946 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.95 % Allowed : 9.69 % Favored : 89.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.28), residues: 854 helix: 0.07 (0.28), residues: 333 sheet: -0.35 (0.57), residues: 87 loop : -1.77 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 279 HIS 0.011 0.001 HIS A 275 PHE 0.015 0.001 PHE A 861 TYR 0.018 0.001 TYR A 531 ARG 0.004 0.000 ARG A 671 *********************** 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 149 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 142 time to evaluate : 0.749 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.8044 (m-70) cc_final: 0.7837 (m170) REVERT: A 234 TRP cc_start: 0.6038 (m100) cc_final: 0.4324 (m100) REVERT: A 262 ARG cc_start: 0.7236 (tmt-80) cc_final: 0.6866 (tpt90) REVERT: A 315 GLU cc_start: 0.8215 (mm-30) cc_final: 0.7998 (mm-30) REVERT: A 360 ILE cc_start: 0.7725 (tt) cc_final: 0.7375 (tt) REVERT: A 386 PHE cc_start: 0.7869 (m-80) cc_final: 0.7486 (m-80) REVERT: A 435 LYS cc_start: 0.7939 (tttt) cc_final: 0.7644 (tttm) REVERT: A 439 MET cc_start: 0.6988 (mmp) cc_final: 0.6459 (mmp) REVERT: A 502 GLU cc_start: 0.7577 (mp0) cc_final: 0.7137 (mp0) REVERT: A 744 LYS cc_start: 0.8507 (tptp) cc_final: 0.8234 (tptp) REVERT: A 803 PHE cc_start: 0.6731 (p90) cc_final: 0.5937 (p90) outliers start: 7 outliers final: 4 residues processed: 145 average time/residue: 0.2027 time to fit residues: 39.1935 Evaluate side-chains 141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 137 time to evaluate : 0.730 ------------------------------------------------------------------------------- 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 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 53 optimal weight: 0.0670 chunk 21 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 84 optimal weight: 0.9990 chunk 69 optimal weight: 0.0170 chunk 77 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 62 optimal weight: 0.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6499 moved from start: 0.2076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7249 Z= 0.185 Angle : 0.558 7.626 9862 Z= 0.290 Chirality : 0.043 0.170 1011 Planarity : 0.004 0.042 1273 Dihedral : 4.788 22.467 946 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.03 % Favored : 92.97 % Rotamer: Outliers : 2.32 % Allowed : 12.96 % Favored : 84.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.28), residues: 854 helix: 0.39 (0.29), residues: 332 sheet: -0.32 (0.58), residues: 87 loop : -1.75 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 850 HIS 0.015 0.001 HIS A 275 PHE 0.021 0.001 PHE A 861 TYR 0.018 0.001 TYR A 531 ARG 0.004 0.000 ARG A 887 *********************** 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 152 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 135 time to evaluate : 0.750 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7985 (m-70) cc_final: 0.7766 (m170) REVERT: A 234 TRP cc_start: 0.6149 (m100) cc_final: 0.4371 (m100) REVERT: A 262 ARG cc_start: 0.7143 (tmt-80) cc_final: 0.6919 (tmt-80) REVERT: A 315 GLU cc_start: 0.8224 (mm-30) cc_final: 0.7931 (mm-30) REVERT: A 502 GLU cc_start: 0.7627 (mp0) cc_final: 0.7212 (mp0) REVERT: A 744 LYS cc_start: 0.8458 (tptp) cc_final: 0.8224 (tptm) REVERT: A 803 PHE cc_start: 0.6710 (p90) cc_final: 0.6005 (p90) REVERT: A 815 ASP cc_start: 0.6326 (t0) cc_final: 0.6069 (t0) outliers start: 17 outliers final: 13 residues processed: 140 average time/residue: 0.2006 time to fit residues: 37.6173 Evaluate side-chains 144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 131 time to evaluate : 0.777 ------------------------------------------------------------------------------- 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 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 Chi-restraints excluded: chain A residue 836 ILE Chi-restraints excluded: chain A residue 886 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 77 optimal weight: 0.4980 chunk 58 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 52 optimal weight: 0.5980 chunk 78 optimal weight: 6.9990 chunk 83 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 902 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6541 moved from start: 0.2361 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= 0.215 Angle : 0.581 7.141 9862 Z= 0.301 Chirality : 0.043 0.160 1011 Planarity : 0.004 0.062 1273 Dihedral : 4.845 22.400 946 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.27 % Allowed : 14.46 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.29), residues: 854 helix: 0.55 (0.30), residues: 325 sheet: -0.41 (0.58), residues: 87 loop : -1.71 (0.29), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 850 HIS 0.010 0.001 HIS A 275 PHE 0.021 0.002 PHE A 861 TYR 0.016 0.002 TYR A 531 ARG 0.004 0.000 ARG A 887 *********************** 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 158 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 134 time to evaluate : 0.689 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7369 (tpp-160) REVERT: A 81 GLN cc_start: 0.7359 (mp10) cc_final: 0.7108 (mp10) REVERT: A 95 HIS cc_start: 0.8021 (m-70) cc_final: 0.7803 (m170) REVERT: A 262 ARG cc_start: 0.7166 (tmt-80) cc_final: 0.6908 (tmt-80) REVERT: A 315 GLU cc_start: 0.8270 (mm-30) cc_final: 0.7962 (mm-30) REVERT: A 390 GLU cc_start: 0.7505 (mp0) cc_final: 0.7293 (mp0) REVERT: A 397 LEU cc_start: 0.7827 (OUTLIER) cc_final: 0.7603 (tt) REVERT: A 436 LYS cc_start: 0.7941 (tptp) cc_final: 0.7592 (tptp) REVERT: A 502 GLU cc_start: 0.7668 (mp0) cc_final: 0.7193 (mp0) REVERT: A 744 LYS cc_start: 0.8460 (tptp) cc_final: 0.8229 (tptm) REVERT: A 803 PHE cc_start: 0.6696 (p90) cc_final: 0.6011 (p90) REVERT: A 815 ASP cc_start: 0.6393 (t0) cc_final: 0.6192 (t0) REVERT: A 900 LYS cc_start: 0.8020 (mtpp) cc_final: 0.7785 (mtpp) REVERT: A 925 PHE cc_start: 0.6192 (OUTLIER) cc_final: 0.5975 (m-10) REVERT: A 941 MET cc_start: 0.4838 (tpp) cc_final: 0.4593 (tpt) outliers start: 24 outliers final: 12 residues processed: 145 average time/residue: 0.1907 time to fit residues: 37.0802 Evaluate side-chains 145 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.749 ------------------------------------------------------------------------------- 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 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 431 MET 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 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 69 optimal weight: 0.0070 chunk 47 optimal weight: 0.5980 chunk 1 optimal weight: 0.0870 chunk 61 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 20 optimal weight: 4.9990 overall best weight: 0.3376 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6472 moved from start: 0.2532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 7249 Z= 0.157 Angle : 0.544 6.754 9862 Z= 0.283 Chirality : 0.042 0.164 1011 Planarity : 0.004 0.046 1273 Dihedral : 4.664 22.055 946 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.32 % Allowed : 15.42 % Favored : 82.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.98 (0.29), residues: 854 helix: 0.72 (0.30), residues: 328 sheet: -1.10 (0.57), residues: 94 loop : -1.67 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 850 HIS 0.012 0.001 HIS A 275 PHE 0.020 0.001 PHE A 861 TYR 0.022 0.001 TYR A 863 ARG 0.002 0.000 ARG A 887 *********************** 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 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6827 (mt-10) cc_final: 0.5889 (pt0) REVERT: A 81 GLN cc_start: 0.7237 (mp10) cc_final: 0.6968 (mp10) REVERT: A 95 HIS cc_start: 0.8019 (m-70) cc_final: 0.7809 (m170) REVERT: A 234 TRP cc_start: 0.6199 (m100) cc_final: 0.4033 (m100) REVERT: A 262 ARG cc_start: 0.7090 (tmt-80) cc_final: 0.6851 (tmt-80) REVERT: A 315 GLU cc_start: 0.8280 (mm-30) cc_final: 0.7938 (mm-30) REVERT: A 397 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7532 (tt) REVERT: A 404 GLU cc_start: 0.7680 (tp30) cc_final: 0.7264 (tp30) REVERT: A 436 LYS cc_start: 0.7861 (tptp) cc_final: 0.7556 (tptp) REVERT: A 744 LYS cc_start: 0.8431 (tptp) cc_final: 0.8222 (tptm) REVERT: A 803 PHE cc_start: 0.6693 (p90) cc_final: 0.6034 (p90) REVERT: A 863 TYR cc_start: 0.6605 (m-10) cc_final: 0.6277 (m-10) REVERT: A 900 LYS cc_start: 0.7972 (mtpp) cc_final: 0.7720 (mtpp) outliers start: 17 outliers final: 11 residues processed: 140 average time/residue: 0.1882 time to fit residues: 35.8142 Evaluate side-chains 142 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 130 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 389 LEU Chi-restraints excluded: chain A residue 394 LEU Chi-restraints excluded: chain A residue 397 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 439 MET 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0670 chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 69 optimal weight: 0.0370 chunk 38 optimal weight: 3.9990 chunk 6 optimal weight: 0.1980 chunk 43 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 overall best weight: 0.4600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 902 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6485 moved from start: 0.2682 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= 0.168 Angle : 0.546 6.795 9862 Z= 0.284 Chirality : 0.042 0.157 1011 Planarity : 0.004 0.047 1273 Dihedral : 4.610 21.687 946 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.56 % Favored : 93.44 % Rotamer: Outliers : 2.86 % Allowed : 15.96 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.29), residues: 854 helix: 0.70 (0.30), residues: 332 sheet: -1.00 (0.54), residues: 102 loop : -1.72 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 850 HIS 0.010 0.001 HIS A 275 PHE 0.022 0.001 PHE A 861 TYR 0.017 0.001 TYR A 863 ARG 0.003 0.000 ARG A 387 *********************** 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 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 130 time to evaluate : 0.710 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 GLU cc_start: 0.6847 (mt-10) cc_final: 0.5935 (pt0) REVERT: A 234 TRP cc_start: 0.6178 (m100) cc_final: 0.4022 (m100) REVERT: A 262 ARG cc_start: 0.7079 (tmt-80) cc_final: 0.6872 (tmt-80) REVERT: A 315 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7892 (mm-30) REVERT: A 397 LEU cc_start: 0.7782 (OUTLIER) cc_final: 0.7567 (tt) REVERT: A 436 LYS cc_start: 0.7839 (tptp) cc_final: 0.7541 (tptp) REVERT: A 502 GLU cc_start: 0.7644 (OUTLIER) cc_final: 0.6808 (mp0) REVERT: A 744 LYS cc_start: 0.8404 (tptp) cc_final: 0.8190 (tptm) REVERT: A 803 PHE cc_start: 0.6688 (p90) cc_final: 0.6056 (p90) REVERT: A 900 LYS cc_start: 0.7964 (mtpp) cc_final: 0.7704 (mtpp) outliers start: 21 outliers final: 15 residues processed: 140 average time/residue: 0.1969 time to fit residues: 37.4470 Evaluate side-chains 141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 124 time to evaluate : 0.754 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 431 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 GLU 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 9 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.2831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 7249 Z= 0.227 Angle : 0.586 7.536 9862 Z= 0.304 Chirality : 0.044 0.162 1011 Planarity : 0.004 0.051 1273 Dihedral : 4.840 21.857 946 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.86 % Allowed : 16.64 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.29), residues: 854 helix: 0.60 (0.30), residues: 332 sheet: -0.84 (0.58), residues: 89 loop : -1.82 (0.29), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP A 850 HIS 0.008 0.001 HIS A 275 PHE 0.021 0.001 PHE A 861 TYR 0.017 0.002 TYR A 219 ARG 0.004 0.000 ARG A 134 *********************** 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 154 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7655 (tpp-160) cc_final: 0.7404 (tpp-160) REVERT: A 52 GLU cc_start: 0.6933 (mt-10) cc_final: 0.5987 (pt0) REVERT: A 234 TRP cc_start: 0.6238 (m100) cc_final: 0.4152 (m100) REVERT: A 262 ARG cc_start: 0.7179 (tmt-80) cc_final: 0.6876 (tpt170) REVERT: A 315 GLU cc_start: 0.8290 (mm-30) cc_final: 0.7868 (mm-30) REVERT: A 386 PHE cc_start: 0.7817 (m-80) cc_final: 0.7609 (m-80) REVERT: A 397 LEU cc_start: 0.7895 (OUTLIER) cc_final: 0.7639 (tt) REVERT: A 404 GLU cc_start: 0.7683 (tp30) cc_final: 0.7257 (tp30) REVERT: A 436 LYS cc_start: 0.7879 (tptp) cc_final: 0.7563 (tptp) REVERT: A 450 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.7565 (t) REVERT: A 744 LYS cc_start: 0.8430 (tptp) cc_final: 0.8224 (tptm) REVERT: A 803 PHE cc_start: 0.6646 (p90) cc_final: 0.5924 (p90) REVERT: A 900 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7787 (mtpp) outliers start: 21 outliers final: 14 residues processed: 143 average time/residue: 0.2188 time to fit residues: 41.5700 Evaluate side-chains 147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 65 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 79 optimal weight: 0.5980 chunk 72 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- 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 ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6570 moved from start: 0.2993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7249 Z= 0.241 Angle : 0.615 10.332 9862 Z= 0.317 Chirality : 0.045 0.171 1011 Planarity : 0.004 0.049 1273 Dihedral : 4.947 22.354 946 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 13.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.86 % Allowed : 18.01 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.18 (0.29), residues: 854 helix: 0.53 (0.30), residues: 334 sheet: -0.89 (0.58), residues: 89 loop : -1.87 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 850 HIS 0.013 0.001 HIS A 95 PHE 0.021 0.001 PHE A 861 TYR 0.021 0.002 TYR A 531 ARG 0.003 0.000 ARG A 134 *********************** 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: 21 poor density : 134 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7686 (tpp-160) cc_final: 0.7419 (tpp-160) REVERT: A 52 GLU cc_start: 0.7016 (mt-10) cc_final: 0.6117 (pt0) REVERT: A 230 GLN cc_start: 0.6906 (tm-30) cc_final: 0.6567 (pt0) REVERT: A 234 TRP cc_start: 0.6223 (m100) cc_final: 0.4184 (m100) REVERT: A 262 ARG cc_start: 0.7227 (tmt-80) cc_final: 0.6867 (tmt-80) REVERT: A 315 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7895 (mm-30) REVERT: A 386 PHE cc_start: 0.7830 (m-80) cc_final: 0.7542 (m-80) REVERT: A 397 LEU cc_start: 0.7929 (OUTLIER) cc_final: 0.7650 (tt) REVERT: A 404 GLU cc_start: 0.7685 (tp30) cc_final: 0.7270 (tp30) REVERT: A 436 LYS cc_start: 0.7888 (tptp) cc_final: 0.7566 (tptp) REVERT: A 450 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.7604 (t) REVERT: A 502 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6795 (mp0) REVERT: A 744 LYS cc_start: 0.8452 (tptp) cc_final: 0.8163 (tptm) REVERT: A 751 ARG cc_start: 0.7009 (ttp80) cc_final: 0.6582 (ttp80) REVERT: A 803 PHE cc_start: 0.6634 (p90) cc_final: 0.5922 (p90) REVERT: A 900 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7780 (mtpp) outliers start: 21 outliers final: 14 residues processed: 144 average time/residue: 0.1957 time to fit residues: 38.3381 Evaluate side-chains 147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 130 time to evaluate : 0.748 ------------------------------------------------------------------------------- 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 397 LEU Chi-restraints excluded: chain A residue 431 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 79 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 50 optimal weight: 0.4980 chunk 81 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 902 HIS ** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6556 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7249 Z= 0.218 Angle : 0.607 12.242 9862 Z= 0.311 Chirality : 0.044 0.170 1011 Planarity : 0.004 0.051 1273 Dihedral : 4.966 22.335 946 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.14 % Favored : 92.86 % Rotamer: Outliers : 2.73 % Allowed : 18.55 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.29), residues: 854 helix: 0.57 (0.30), residues: 335 sheet: -1.00 (0.56), residues: 94 loop : -1.86 (0.29), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP A 850 HIS 0.007 0.001 HIS A 275 PHE 0.022 0.001 PHE A 861 TYR 0.019 0.002 TYR A 531 ARG 0.003 0.000 ARG A 134 *********************** 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 150 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 130 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7665 (tpp-160) cc_final: 0.7390 (tpp-160) REVERT: A 52 GLU cc_start: 0.7024 (mt-10) cc_final: 0.6119 (pt0) REVERT: A 230 GLN cc_start: 0.6846 (tm-30) cc_final: 0.6613 (pt0) REVERT: A 234 TRP cc_start: 0.6235 (m100) cc_final: 0.4199 (m100) REVERT: A 262 ARG cc_start: 0.7201 (tmt-80) cc_final: 0.6818 (tmt-80) REVERT: A 315 GLU cc_start: 0.8266 (mm-30) cc_final: 0.7882 (mm-30) REVERT: A 397 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7618 (tt) REVERT: A 404 GLU cc_start: 0.7684 (tp30) cc_final: 0.7203 (tp30) REVERT: A 436 LYS cc_start: 0.7871 (tptp) cc_final: 0.7629 (tptm) REVERT: A 450 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.7569 (t) REVERT: A 502 GLU cc_start: 0.7688 (OUTLIER) cc_final: 0.6784 (mp0) REVERT: A 744 LYS cc_start: 0.8440 (tptp) cc_final: 0.8151 (tptm) REVERT: A 751 ARG cc_start: 0.6976 (ttp80) cc_final: 0.6542 (ttp80) REVERT: A 803 PHE cc_start: 0.6670 (p90) cc_final: 0.5956 (p90) REVERT: A 900 LYS cc_start: 0.7997 (mtpp) cc_final: 0.7742 (mtpp) outliers start: 20 outliers final: 15 residues processed: 138 average time/residue: 0.1952 time to fit residues: 36.4006 Evaluate side-chains 147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 151 ILE 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 431 MET Chi-restraints excluded: chain A residue 439 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 747 GLU Chi-restraints excluded: chain A residue 866 LEU Chi-restraints excluded: chain A residue 899 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 38 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 41 optimal weight: 0.0970 chunk 54 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 20 optimal weight: 0.0370 overall best weight: 0.5056 ------------------------------------------------------------------------------- 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 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6513 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7249 Z= 0.184 Angle : 0.590 11.486 9862 Z= 0.302 Chirality : 0.043 0.160 1011 Planarity : 0.004 0.052 1273 Dihedral : 4.815 21.979 946 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 12.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.46 % Allowed : 19.10 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 854 helix: 0.62 (0.30), residues: 336 sheet: -0.67 (0.55), residues: 100 loop : -1.89 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 850 HIS 0.008 0.001 HIS A 275 PHE 0.023 0.001 PHE A 861 TYR 0.018 0.001 TYR A 531 ARG 0.003 0.000 ARG A 134 ********************** 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 151 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 133 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 ARG cc_start: 0.7626 (tpp-160) cc_final: 0.7364 (tpp-160) REVERT: A 52 GLU cc_start: 0.6982 (mt-10) cc_final: 0.6045 (pt0) REVERT: A 188 VAL cc_start: 0.7947 (t) cc_final: 0.7717 (p) REVERT: A 234 TRP cc_start: 0.6139 (m100) cc_final: 0.4178 (m100) REVERT: A 262 ARG cc_start: 0.7151 (tmt-80) cc_final: 0.6772 (tmt-80) REVERT: A 315 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7870 (mm-30) REVERT: A 397 LEU cc_start: 0.7825 (OUTLIER) cc_final: 0.7582 (tt) REVERT: A 404 GLU cc_start: 0.7680 (tp30) cc_final: 0.7224 (tp30) REVERT: A 436 LYS cc_start: 0.7813 (tptp) cc_final: 0.7572 (tptp) REVERT: A 502 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.6840 (mp0) REVERT: A 645 GLN cc_start: 0.7608 (mt0) cc_final: 0.7376 (mt0) REVERT: A 744 LYS cc_start: 0.8419 (tptp) cc_final: 0.8197 (tptm) REVERT: A 803 PHE cc_start: 0.6687 (p90) cc_final: 0.5977 (p90) REVERT: A 900 LYS cc_start: 0.7963 (mtpp) cc_final: 0.7691 (mtpp) outliers start: 18 outliers final: 13 residues processed: 142 average time/residue: 0.1900 time to fit residues: 36.7257 Evaluate side-chains 145 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 242 VAL 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 431 MET Chi-restraints excluded: chain A residue 442 LEU Chi-restraints excluded: chain A residue 450 VAL Chi-restraints excluded: chain A residue 502 GLU Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 662 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 62 optimal weight: 0.0970 chunk 10 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 68 optimal weight: 3.9990 chunk 28 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 943 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 = 0.4503 r_free = 0.4503 target = 0.196736 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4280 r_free = 0.4280 target = 0.175525 restraints weight = 10977.073| |-----------------------------------------------------------------------------| r_work (start): 0.4288 rms_B_bonded: 3.66 r_work: 0.4152 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.4152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6519 moved from start: 0.3193 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= 0.198 Angle : 0.598 11.554 9862 Z= 0.306 Chirality : 0.043 0.160 1011 Planarity : 0.004 0.052 1273 Dihedral : 4.841 21.804 946 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.49 % Favored : 92.51 % Rotamer: Outliers : 2.59 % Allowed : 18.69 % Favored : 78.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.29), residues: 854 helix: 0.64 (0.30), residues: 335 sheet: -0.72 (0.55), residues: 100 loop : -1.88 (0.29), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 850 HIS 0.006 0.001 HIS A 943 PHE 0.022 0.001 PHE A 861 TYR 0.019 0.002 TYR A 531 ARG 0.003 0.000 ARG A 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1959.75 seconds wall clock time: 36 minutes 34.84 seconds (2194.84 seconds total)