Starting phenix.real_space_refine on Fri Aug 7 13:27:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877_trim.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3y_18877/08_2026/8r3y_18877.map" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2467 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 6 5.49 5 S 45 5.16 5 C 6423 2.51 5 N 1763 2.21 5 O 1895 1.98 5 H 9975 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 78 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 20107 Number of models: 1 Model: "" Number of chains: 4 Chain: "I" Number of atoms: 5418 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 5418 Classifications: {'peptide': 338} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 16, 'TRANS': 321} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "L" Number of atoms: 13174 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 13174 Classifications: {'peptide': 861} Modifications used: {'NH3': 1} Link IDs: {'PCIS': 1, 'PTRANS': 54, 'TRANS': 805} Chain breaks: 5 Chain: "P" Number of atoms: 1484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1484 Classifications: {'peptide': 94} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain breaks: 1 Chain: "I" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.29, per 1000 atoms: 0.16 Number of scatterers: 20107 At special positions: 0 Unit cell: (87.74, 108.24, 118.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 45 16.00 P 6 15.00 O 1895 8.00 N 1763 7.00 C 6423 6.00 H 9975 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.88 Conformation dependent library (CDL) restraints added in 479.3 milliseconds 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2390 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 21 sheets defined 17.4% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'I' and resid 250 through 254 removed outlier: 3.549A pdb=" N PHE I 254 " --> pdb=" O LEU I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 292 through 309 Processing helix chain 'I' and resid 339 through 348 Processing helix chain 'I' and resid 351 through 373 removed outlier: 4.001A pdb=" N PHE I 357 " --> pdb=" O GLU I 353 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N TYR I 358 " --> pdb=" O HIS I 354 " (cutoff:3.500A) Processing helix chain 'I' and resid 421 through 427 removed outlier: 3.787A pdb=" N LEU I 425 " --> pdb=" O ALA I 421 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY I 427 " --> pdb=" O GLU I 423 " (cutoff:3.500A) Processing helix chain 'I' and resid 432 through 449 removed outlier: 3.741A pdb=" N TRP I 436 " --> pdb=" O PHE I 432 " (cutoff:3.500A) Processing helix chain 'I' and resid 466 through 477 removed outlier: 3.749A pdb=" N GLN I 472 " --> pdb=" O ASP I 468 " (cutoff:3.500A) Processing helix chain 'I' and resid 486 through 498 Processing helix chain 'I' and resid 511 through 519 Processing helix chain 'I' and resid 519 through 524 removed outlier: 3.904A pdb=" N ASN I 524 " --> pdb=" O PRO I 520 " (cutoff:3.500A) Processing helix chain 'I' and resid 526 through 532 Processing helix chain 'I' and resid 548 through 552 Processing helix chain 'I' and resid 553 through 558 Processing helix chain 'I' and resid 569 through 574 removed outlier: 4.226A pdb=" N LYS I 573 " --> pdb=" O ASP I 569 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 21 removed outlier: 3.594A pdb=" N GLU L 21 " --> pdb=" O LEU L 18 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 184 removed outlier: 3.580A pdb=" N VAL L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N SER L 184 " --> pdb=" O GLU L 180 " (cutoff:3.500A) Processing helix chain 'L' and resid 313 through 318 removed outlier: 3.532A pdb=" N GLY L 318 " --> pdb=" O ARG L 314 " (cutoff:3.500A) Processing helix chain 'L' and resid 389 through 393 removed outlier: 4.430A pdb=" N SER L 393 " --> pdb=" O LEU L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 420 Processing helix chain 'L' and resid 476 through 479 Processing helix chain 'L' and resid 524 through 526 No H-bonds generated for 'chain 'L' and resid 524 through 526' Processing helix chain 'L' and resid 807 through 811 Processing helix chain 'L' and resid 849 through 853 Processing helix chain 'L' and resid 908 through 913 Processing helix chain 'P' and resid 201 through 206 Processing helix chain 'P' and resid 227 through 237 removed outlier: 3.721A pdb=" N ALA P 237 " --> pdb=" O ASP P 233 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 255 through 262 removed outlier: 7.370A pdb=" N LEU I 257 " --> pdb=" O ARG I 272 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ARG I 272 " --> pdb=" O LEU I 257 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N VAL I 259 " --> pdb=" O LEU I 270 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N LEU I 270 " --> pdb=" O VAL I 259 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 384 through 386 Processing sheet with id=AA3, first strand: chain 'I' and resid 481 through 482 removed outlier: 6.348A pdb=" N ILE I 481 " --> pdb=" O SER L 510 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'L' and resid 23 through 31 removed outlier: 4.602A pdb=" N ALA L 24 " --> pdb=" O SER L 938 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N SER L 938 " --> pdb=" O ALA L 24 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ARG L 934 " --> pdb=" O THR L 28 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N GLU L 30 " --> pdb=" O PHE L 932 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N PHE L 932 " --> pdb=" O GLU L 30 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU L 931 " --> pdb=" O ILE L 927 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ILE L 927 " --> pdb=" O GLU L 931 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N GLN L 922 " --> pdb=" O THR L 918 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 37 through 43 removed outlier: 6.487A pdb=" N GLY L 52 " --> pdb=" O SER L 38 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N LEU L 40 " --> pdb=" O ALA L 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ALA L 50 " --> pdb=" O LEU L 40 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N PHE L 42 " --> pdb=" O ILE L 48 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N ILE L 48 " --> pdb=" O PHE L 42 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ALA L 57 " --> pdb=" O THR L 53 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 78 through 83 removed outlier: 3.675A pdb=" N GLN L 80 " --> pdb=" O LEU L 93 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N SER L 92 " --> pdb=" O HIS L 100 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N HIS L 100 " --> pdb=" O SER L 92 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU L 99 " --> pdb=" O SER L 118 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N SER L 118 " --> pdb=" O LEU L 99 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N LEU L 101 " --> pdb=" O ALA L 116 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 141 through 144 removed outlier: 6.291A pdb=" N GLN L 174 " --> pdb=" O PHE L 162 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 198 through 202 removed outlier: 4.531A pdb=" N LEU L 201 " --> pdb=" O LEU L 212 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU L 212 " --> pdb=" O LEU L 201 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N LEU L 220 " --> pdb=" O ILE L 233 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N ILE L 233 " --> pdb=" O LEU L 220 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ILE L 222 " --> pdb=" O ASP L 231 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 240 through 243 removed outlier: 5.180A pdb=" N SER L 255 " --> pdb=" O GLU L 241 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N LEU L 243 " --> pdb=" O VAL L 253 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N VAL L 253 " --> pdb=" O LEU L 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 291 through 296 removed outlier: 4.223A pdb=" N LYS L 293 " --> pdb=" O SER L 309 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N CYS L 322 " --> pdb=" O GLY L 310 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N HIS L 321 " --> pdb=" O PHE L 336 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 340 through 345 removed outlier: 3.542A pdb=" N ASP L 342 " --> pdb=" O LEU L 364 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 395 through 401 removed outlier: 3.860A pdb=" N THR L 456 " --> pdb=" O HIS L 452 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL L 457 " --> pdb=" O LYS L 472 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N LYS L 472 " --> pdb=" O VAL L 457 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N PHE L 459 " --> pdb=" O LEU L 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 436 through 437 Processing sheet with id=AB5, first strand: chain 'L' and resid 517 through 523 removed outlier: 3.689A pdb=" N GLN L 528 " --> pdb=" O CYS L 523 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N GLN L 537 " --> pdb=" O GLY L 533 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N VAL L 538 " --> pdb=" O LEU L 592 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N LEU L 592 " --> pdb=" O VAL L 538 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N VAL L 540 " --> pdb=" O ARG L 590 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N SER L 553 " --> pdb=" O ARG L 590 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 548 through 550 Processing sheet with id=AB7, first strand: chain 'L' and resid 603 through 607 removed outlier: 3.570A pdb=" N LEU L 612 " --> pdb=" O HIS L 607 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N ASP L 625 " --> pdb=" O PRO L 631 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 707 through 709 removed outlier: 10.816A pdb=" N GLU P 217 " --> pdb=" O PRO P 190 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE P 192 " --> pdb=" O ILE P 215 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N THR P 245 " --> pdb=" O LEU P 216 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N VAL P 218 " --> pdb=" O ILE P 243 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N ILE P 243 " --> pdb=" O VAL P 218 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU P 242 " --> pdb=" O LEU P 160 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG P 156 " --> pdb=" O VAL P 246 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 707 through 709 removed outlier: 10.816A pdb=" N GLU P 217 " --> pdb=" O PRO P 190 " (cutoff:3.500A) removed outlier: 4.802A pdb=" N ILE P 192 " --> pdb=" O ILE P 215 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 723 through 731 removed outlier: 3.530A pdb=" N CYS L 725 " --> pdb=" O GLY L 746 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY L 740 " --> pdb=" O THR L 731 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N PHE L 753 " --> pdb=" O ALA L 745 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER L 751 " --> pdb=" O THR L 747 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL L 752 " --> pdb=" O GLU L 781 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N GLU L 781 " --> pdb=" O VAL L 752 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ALA L 754 " --> pdb=" O GLY L 779 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU L 775 " --> pdb=" O GLU L 758 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'L' and resid 790 through 796 removed outlier: 3.589A pdb=" N ALA L 792 " --> pdb=" O ALA L 828 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N GLN L 832 " --> pdb=" O SER L 829 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N THR L 845 " --> pdb=" O VAL L 835 " (cutoff:3.500A) removed outlier: 7.534A pdb=" N THR L 837 " --> pdb=" O ALA L 843 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N ALA L 843 " --> pdb=" O THR L 837 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 857 through 866 removed outlier: 6.686A pdb=" N LEU L 881 " --> pdb=" O ARG L 858 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL L 860 " --> pdb=" O ALA L 879 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA L 879 " --> pdb=" O VAL L 860 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N LEU L 862 " --> pdb=" O CYS L 877 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N CYS L 877 " --> pdb=" O LEU L 862 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N THR L 864 " --> pdb=" O GLU L 875 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N GLU L 875 " --> pdb=" O THR L 864 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N VAL L 887 " --> pdb=" O HIS L 900 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N HIS L 900 " --> pdb=" O VAL L 887 " (cutoff:3.500A) removed outlier: 6.901A pdb=" N VAL L 889 " --> pdb=" O GLN L 898 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARG L 896 " --> pdb=" O SER L 891 " (cutoff:3.500A) 324 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.50 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.91 - 1.10: 9950 1.10 - 1.28: 1684 1.28 - 1.46: 3152 1.46 - 1.64: 5495 1.64 - 1.82: 65 Bond restraints: 20346 Sorted by residual: bond pdb=" N3B ANP I 601 " pdb=" PG ANP I 601 " ideal model delta sigma weight residual 1.795 1.568 0.227 2.00e-02 2.50e+03 1.28e+02 bond pdb=" NE2 GLN P 230 " pdb="HE21 GLN P 230 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 PHE L 83 " pdb=" HE1 PHE L 83 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N ASP L 248 " pdb=" H ASP L 248 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" N ASN L 883 " pdb=" H ASN L 883 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 ... (remaining 20341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.86: 31479 2.86 - 5.71: 4274 5.71 - 8.57: 965 8.57 - 11.43: 28 11.43 - 14.28: 24 Bond angle restraints: 36770 Sorted by residual: angle pdb=" CA PHE I 322 " pdb=" CB PHE I 322 " pdb=" CG PHE I 322 " ideal model delta sigma weight residual 113.80 119.84 -6.04 1.00e+00 1.00e+00 3.65e+01 angle pdb=" N THR I 395 " pdb=" CA THR I 395 " pdb=" C THR I 395 " ideal model delta sigma weight residual 114.09 123.09 -9.00 1.55e+00 4.16e-01 3.37e+01 angle pdb=" CA ASP L 908 " pdb=" CB ASP L 908 " pdb=" CG ASP L 908 " ideal model delta sigma weight residual 112.60 118.30 -5.70 1.00e+00 1.00e+00 3.25e+01 angle pdb=" CA ASP L 357 " pdb=" CB ASP L 357 " pdb=" CG ASP L 357 " ideal model delta sigma weight residual 112.60 118.19 -5.59 1.00e+00 1.00e+00 3.12e+01 angle pdb=" CB HIS L 72 " pdb=" CG HIS L 72 " pdb=" CD2 HIS L 72 " ideal model delta sigma weight residual 131.20 124.21 6.99 1.30e+00 5.92e-01 2.89e+01 ... (remaining 36765 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 8503 17.81 - 35.63: 690 35.63 - 53.44: 226 53.44 - 71.25: 180 71.25 - 89.07: 22 Dihedral angle restraints: 9621 sinusoidal: 5243 harmonic: 4378 Sorted by residual: dihedral pdb=" CD ARG I 377 " pdb=" NE ARG I 377 " pdb=" CZ ARG I 377 " pdb=" NH1 ARG I 377 " ideal model delta sinusoidal sigma weight residual 0.00 -54.52 54.52 1 1.00e+01 1.00e-02 4.03e+01 dihedral pdb=" CA LEU I 563 " pdb=" C LEU I 563 " pdb=" N TPO I 564 " pdb=" CA TPO I 564 " ideal model delta harmonic sigma weight residual -180.00 -150.03 -29.97 0 5.00e+00 4.00e-02 3.59e+01 dihedral pdb=" CA GLN L 662 " pdb=" C GLN L 662 " pdb=" N SEP L 663 " pdb=" CA SEP L 663 " ideal model delta harmonic sigma weight residual 180.00 150.21 29.79 0 5.00e+00 4.00e-02 3.55e+01 ... (remaining 9618 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 1104 0.107 - 0.213: 399 0.213 - 0.320: 52 0.320 - 0.426: 12 0.426 - 0.533: 3 Chirality restraints: 1570 Sorted by residual: chirality pdb=" CA HIS L 391 " pdb=" N HIS L 391 " pdb=" C HIS L 391 " pdb=" CB HIS L 391 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.09e+00 chirality pdb=" CA SER L 611 " pdb=" N SER L 611 " pdb=" C SER L 611 " pdb=" CB SER L 611 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 chirality pdb=" CA LEU I 497 " pdb=" N LEU I 497 " pdb=" C LEU I 497 " pdb=" CB LEU I 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.77e+00 ... (remaining 1567 not shown) Planarity restraints: 3037 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 610 " -0.281 2.00e-02 2.50e+03 1.11e-01 4.90e+02 pdb=" CG TRP L 610 " -0.074 2.00e-02 2.50e+03 pdb=" CD1 TRP L 610 " 0.044 2.00e-02 2.50e+03 pdb=" CD2 TRP L 610 " 0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP L 610 " 0.098 2.00e-02 2.50e+03 pdb=" CE2 TRP L 610 " 0.022 2.00e-02 2.50e+03 pdb=" CE3 TRP L 610 " 0.085 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 610 " -0.063 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 610 " 0.052 2.00e-02 2.50e+03 pdb=" CH2 TRP L 610 " -0.071 2.00e-02 2.50e+03 pdb=" HD1 TRP L 610 " 0.033 2.00e-02 2.50e+03 pdb=" HE1 TRP L 610 " 0.143 2.00e-02 2.50e+03 pdb=" HE3 TRP L 610 " 0.125 2.00e-02 2.50e+03 pdb=" HZ2 TRP L 610 " -0.113 2.00e-02 2.50e+03 pdb=" HZ3 TRP L 610 " 0.103 2.00e-02 2.50e+03 pdb=" HH2 TRP L 610 " -0.138 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG L 247 " -0.500 9.50e-02 1.11e+02 2.07e-01 3.67e+02 pdb=" NE ARG L 247 " -0.104 2.00e-02 2.50e+03 pdb=" CZ ARG L 247 " -0.080 2.00e-02 2.50e+03 pdb=" NH1 ARG L 247 " -0.065 2.00e-02 2.50e+03 pdb=" NH2 ARG L 247 " -0.049 2.00e-02 2.50e+03 pdb="HH11 ARG L 247 " 0.263 2.00e-02 2.50e+03 pdb="HH12 ARG L 247 " -0.118 2.00e-02 2.50e+03 pdb="HH21 ARG L 247 " 0.170 2.00e-02 2.50e+03 pdb="HH22 ARG L 247 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG I 262 " 0.320 9.50e-02 1.11e+02 1.46e-01 2.37e+02 pdb=" NE ARG I 262 " 0.020 2.00e-02 2.50e+03 pdb=" CZ ARG I 262 " -0.023 2.00e-02 2.50e+03 pdb=" NH1 ARG I 262 " -0.026 2.00e-02 2.50e+03 pdb=" NH2 ARG I 262 " -0.071 2.00e-02 2.50e+03 pdb="HH11 ARG I 262 " -0.146 2.00e-02 2.50e+03 pdb="HH12 ARG I 262 " 0.083 2.00e-02 2.50e+03 pdb="HH21 ARG I 262 " -0.075 2.00e-02 2.50e+03 pdb="HH22 ARG I 262 " 0.224 2.00e-02 2.50e+03 ... (remaining 3034 not shown) Histogram of nonbonded interaction distances: 1.57 - 2.18: 1370 2.18 - 2.78: 34733 2.78 - 3.39: 55921 3.39 - 3.99: 75901 3.99 - 4.60: 110109 Nonbonded interactions: 278034 Sorted by model distance: nonbonded pdb=" OD2 ASP L 96 " pdb=" HG SER L 98 " model vdw 1.574 2.450 nonbonded pdb=" OD1 ASP I 468 " pdb=" HG SER L 659 " model vdw 1.593 2.450 nonbonded pdb=" OD1 ASP L 164 " pdb=" HG1 THR L 166 " model vdw 1.602 2.450 nonbonded pdb=" HG1 THR I 410 " pdb=" O1P TPO I 412 " model vdw 1.608 2.450 nonbonded pdb=" O TPO I 412 " pdb=" HH TYR I 430 " model vdw 1.625 2.450 ... (remaining 278029 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 1.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 18.960 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.040 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:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6942 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 : 0.013 0.227 10371 Z= 0.805 Angle : 1.983 12.370 14093 Z= 1.296 Chirality : 0.107 0.533 1570 Planarity : 0.018 0.381 1827 Dihedral : 15.128 89.068 3801 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 0.45 Ramachandran Plot: Outliers : 0.32 % Allowed : 7.42 % Favored : 92.26 % Rotamer: Outliers : 3.01 % Allowed : 8.39 % Favored : 88.59 % Cbeta Deviations : 0.92 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.59 (0.22), residues: 1266 helix: -1.86 (0.31), residues: 160 sheet: -0.18 (0.28), residues: 328 loop : -1.28 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG L 858 TYR 0.192 0.021 TYR L 261 PHE 0.092 0.016 PHE I 322 TRP 0.166 0.026 TRP L 610 HIS 0.014 0.003 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.01324 / 0.80 (10371) covalent geometry : angle 1.98333 / 1.30 (14093) hydrogen bonds : bond 0.18374 / 12.33 ( 315) hydrogen bonds : angle 8.96636 / 6.45 ( 879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 282 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 282 MET cc_start: 0.7642 (ttp) cc_final: 0.7441 (ttp) REVERT: I 341 MET cc_start: 0.7222 (ttm) cc_final: 0.7008 (ttm) REVERT: I 410 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5312 (t) REVERT: I 529 MET cc_start: 0.6240 (mtp) cc_final: 0.6010 (mtt) REVERT: L 92 SER cc_start: 0.7455 (t) cc_final: 0.7219 (t) REVERT: L 277 THR cc_start: 0.6159 (m) cc_final: 0.5942 (m) REVERT: L 326 LEU cc_start: 0.5536 (tp) cc_final: 0.5239 (tp) REVERT: L 730 ASP cc_start: 0.8146 (t0) cc_final: 0.7806 (t0) REVERT: L 743 MET cc_start: 0.7970 (tmt) cc_final: 0.7366 (tmt) outliers start: 33 outliers final: 15 residues processed: 303 average time/residue: 0.2477 time to fit residues: 102.5054 Evaluate side-chains 229 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 213 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 335 VAL Chi-restraints excluded: chain I residue 401 LYS Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 542 ASN Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 626 TYR Chi-restraints excluded: chain L residue 660 LEU Chi-restraints excluded: chain L residue 778 LEU Chi-restraints excluded: chain L residue 856 ARG Chi-restraints excluded: chain P residue 241 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 336 ASN I 472 GLN L 112 HIS L 518 GLN L 607 HIS L 707 GLN L 786 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.183842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160498 restraints weight = 40275.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.165585 restraints weight = 18813.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.168730 restraints weight = 11186.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3882 r_free = 0.3882 target = 0.170685 restraints weight = 7860.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.171966 restraints weight = 6200.692| |-----------------------------------------------------------------------------| r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10371 Z= 0.173 Angle : 0.806 7.681 14093 Z= 0.424 Chirality : 0.047 0.212 1570 Planarity : 0.007 0.176 1827 Dihedral : 9.379 65.220 1459 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.13 % Favored : 94.79 % Rotamer: Outliers : 2.65 % Allowed : 12.59 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.49 (0.22), residues: 1266 helix: -0.43 (0.38), residues: 161 sheet: -0.50 (0.26), residues: 346 loop : -1.37 (0.21), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG I 377 TYR 0.024 0.002 TYR L 261 PHE 0.031 0.002 PHE I 552 TRP 0.026 0.002 TRP I 298 HIS 0.008 0.001 HIS P 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00388 / 0.17 (10371) covalent geometry : angle 0.80582 / 0.42 (14093) hydrogen bonds : bond 0.05830 / 3.74 ( 315) hydrogen bonds : angle 7.17148 / 5.21 ( 879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 205 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 282 MET cc_start: 0.7627 (ttp) cc_final: 0.7400 (ttp) REVERT: I 401 LYS cc_start: 0.4018 (OUTLIER) cc_final: 0.3795 (tppt) REVERT: I 487 VAL cc_start: 0.8208 (m) cc_final: 0.7953 (p) REVERT: L 92 SER cc_start: 0.7522 (t) cc_final: 0.7289 (t) REVERT: L 206 ARG cc_start: 0.5393 (ttm-80) cc_final: 0.4883 (ttm110) REVERT: L 326 LEU cc_start: 0.5641 (tp) cc_final: 0.5344 (tp) REVERT: L 386 TYR cc_start: 0.8103 (p90) cc_final: 0.7865 (p90) REVERT: L 743 MET cc_start: 0.7997 (tmt) cc_final: 0.7517 (tmt) REVERT: P 229 ASP cc_start: 0.4686 (OUTLIER) cc_final: 0.4454 (m-30) outliers start: 29 outliers final: 19 residues processed: 224 average time/residue: 0.2005 time to fit residues: 64.2007 Evaluate side-chains 213 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 335 VAL Chi-restraints excluded: chain I residue 401 LYS Chi-restraints excluded: chain I residue 491 SER Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 626 TYR Chi-restraints excluded: chain L residue 778 LEU Chi-restraints excluded: chain L residue 889 VAL Chi-restraints excluded: chain P residue 229 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 0.0670 chunk 27 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 76 optimal weight: 0.7980 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 4.9990 chunk 31 optimal weight: 0.0470 chunk 81 optimal weight: 2.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 336 ASN I 383 ASN I 418 ASN L 80 GLN L 783 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4023 r_free = 0.4023 target = 0.182930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.159693 restraints weight = 40672.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164698 restraints weight = 18843.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.167855 restraints weight = 11181.860| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3875 r_free = 0.3875 target = 0.169832 restraints weight = 7797.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.171070 restraints weight = 6110.871| |-----------------------------------------------------------------------------| r_work (final): 0.3903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6929 moved from start: 0.3458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10371 Z= 0.119 Angle : 0.635 6.325 14093 Z= 0.330 Chirality : 0.045 0.148 1570 Planarity : 0.005 0.044 1827 Dihedral : 8.115 67.808 1448 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.10 % Allowed : 14.05 % Favored : 83.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.22), residues: 1266 helix: 0.03 (0.41), residues: 161 sheet: -0.65 (0.25), residues: 382 loop : -1.35 (0.22), residues: 723 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 73 TYR 0.017 0.001 TYR I 368 PHE 0.015 0.001 PHE I 552 TRP 0.014 0.001 TRP I 298 HIS 0.006 0.001 HIS P 155 Details of bonding type rmsd/Z covalent geometry : bond 0.00254 / 0.12 (10371) covalent geometry : angle 0.63496 / 0.33 (14093) hydrogen bonds : bond 0.04236 / 2.71 ( 315) hydrogen bonds : angle 6.36213 / 4.61 ( 879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 195 time to evaluate : 0.398 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 61 TYR cc_start: 0.7242 (m-80) cc_final: 0.6998 (m-80) REVERT: L 92 SER cc_start: 0.7486 (t) cc_final: 0.7229 (t) REVERT: L 206 ARG cc_start: 0.5379 (ttm-80) cc_final: 0.5034 (ttm110) REVERT: L 326 LEU cc_start: 0.5703 (tp) cc_final: 0.5399 (tp) REVERT: L 626 TYR cc_start: 0.8315 (OUTLIER) cc_final: 0.7900 (p90) REVERT: L 743 MET cc_start: 0.7933 (tmt) cc_final: 0.7571 (tmt) REVERT: L 818 ASP cc_start: 0.8027 (t0) cc_final: 0.7689 (t70) REVERT: P 160 LEU cc_start: 0.7829 (tt) cc_final: 0.7279 (mp) outliers start: 23 outliers final: 17 residues processed: 213 average time/residue: 0.1830 time to fit residues: 57.0419 Evaluate side-chains 197 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 179 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 322 PHE Chi-restraints excluded: chain I residue 335 VAL Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 392 SER Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 626 TYR Chi-restraints excluded: chain P residue 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 7 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 63 optimal weight: 4.9990 chunk 117 optimal weight: 3.9990 chunk 121 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 111 optimal weight: 2.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 336 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.177911 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.155099 restraints weight = 41073.638| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.160060 restraints weight = 19220.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163157 restraints weight = 11377.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.165060 restraints weight = 7937.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.166243 restraints weight = 6227.656| |-----------------------------------------------------------------------------| r_work (final): 0.3835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7062 moved from start: 0.3830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 10371 Z= 0.206 Angle : 0.664 6.501 14093 Z= 0.347 Chirality : 0.045 0.183 1570 Planarity : 0.005 0.046 1827 Dihedral : 8.030 74.711 1442 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 2.55 % Allowed : 15.15 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.72 (0.22), residues: 1266 helix: -0.26 (0.39), residues: 167 sheet: -0.73 (0.26), residues: 364 loop : -1.59 (0.21), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 858 TYR 0.021 0.002 TYR L 261 PHE 0.017 0.002 PHE L 621 TRP 0.029 0.002 TRP L 102 HIS 0.008 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.21 (10371) covalent geometry : angle 0.66386 / 0.35 (14093) hydrogen bonds : bond 0.04658 / 3.00 ( 315) hydrogen bonds : angle 6.40343 / 4.61 ( 879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 PHE cc_start: 0.8985 (t80) cc_final: 0.8690 (t80) REVERT: L 92 SER cc_start: 0.7714 (t) cc_final: 0.7467 (t) REVERT: L 206 ARG cc_start: 0.5341 (ttm-80) cc_final: 0.5055 (ttm110) REVERT: L 626 TYR cc_start: 0.8645 (OUTLIER) cc_final: 0.8069 (p90) REVERT: L 730 ASP cc_start: 0.8229 (t0) cc_final: 0.7566 (t70) REVERT: P 160 LEU cc_start: 0.7867 (tt) cc_final: 0.7319 (mp) outliers start: 28 outliers final: 22 residues processed: 207 average time/residue: 0.1979 time to fit residues: 58.4979 Evaluate side-chains 201 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 335 VAL Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 626 TYR Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 85 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 105 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 100 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 97 optimal weight: 2.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 336 ASN I 383 ASN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN L 204 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.177255 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.155219 restraints weight = 40951.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.160029 restraints weight = 19503.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.162994 restraints weight = 11631.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.164859 restraints weight = 8150.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.165775 restraints weight = 6394.000| |-----------------------------------------------------------------------------| r_work (final): 0.3820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10371 Z= 0.197 Angle : 0.650 8.104 14093 Z= 0.339 Chirality : 0.045 0.152 1570 Planarity : 0.005 0.052 1827 Dihedral : 8.006 80.668 1442 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 4.11 % Allowed : 15.15 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.93 (0.22), residues: 1266 helix: -0.40 (0.39), residues: 167 sheet: -0.91 (0.26), residues: 359 loop : -1.71 (0.21), residues: 740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG L 940 TYR 0.018 0.002 TYR L 261 PHE 0.024 0.002 PHE I 322 TRP 0.015 0.002 TRP I 298 HIS 0.009 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.20 (10371) covalent geometry : angle 0.65048 / 0.34 (14093) hydrogen bonds : bond 0.04536 / 2.96 ( 315) hydrogen bonds : angle 6.39756 / 4.59 ( 879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 183 time to evaluate : 0.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 GLN cc_start: 0.7457 (tm-30) cc_final: 0.7226 (tm-30) REVERT: L 33 PHE cc_start: 0.8971 (t80) cc_final: 0.8631 (t80) REVERT: L 92 SER cc_start: 0.7813 (t) cc_final: 0.7594 (t) REVERT: L 626 TYR cc_start: 0.8657 (OUTLIER) cc_final: 0.7925 (p90) REVERT: L 641 ASN cc_start: 0.7580 (p0) cc_final: 0.7350 (p0) REVERT: L 730 ASP cc_start: 0.8228 (t0) cc_final: 0.7607 (t70) REVERT: L 803 LEU cc_start: 0.6630 (OUTLIER) cc_final: 0.6270 (mt) REVERT: P 160 LEU cc_start: 0.7910 (tt) cc_final: 0.7416 (mp) outliers start: 45 outliers final: 28 residues processed: 212 average time/residue: 0.1855 time to fit residues: 57.3604 Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 204 HIS Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 626 TYR Chi-restraints excluded: chain L residue 658 LYS Chi-restraints excluded: chain L residue 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 76 optimal weight: 0.9990 chunk 90 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 11 optimal weight: 0.5980 chunk 98 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 124 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 overall best weight: 1.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 204 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 = 0.3940 r_free = 0.3940 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.153311 restraints weight = 41329.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.158081 restraints weight = 19431.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161071 restraints weight = 11584.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162900 restraints weight = 8107.172| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.164115 restraints weight = 6402.328| |-----------------------------------------------------------------------------| r_work (final): 0.3807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.4350 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10371 Z= 0.199 Angle : 0.648 6.194 14093 Z= 0.338 Chirality : 0.045 0.165 1570 Planarity : 0.005 0.045 1827 Dihedral : 7.775 83.006 1441 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.47 % Allowed : 16.15 % Favored : 80.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.22), residues: 1266 helix: -0.37 (0.39), residues: 167 sheet: -0.93 (0.27), residues: 357 loop : -1.78 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 940 TYR 0.018 0.002 TYR L 261 PHE 0.019 0.002 PHE I 322 TRP 0.015 0.002 TRP I 298 HIS 0.013 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00445 / 0.20 (10371) covalent geometry : angle 0.64756 / 0.34 (14093) hydrogen bonds : bond 0.04404 / 2.87 ( 315) hydrogen bonds : angle 6.41069 / 4.59 ( 879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 0.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 GLN cc_start: 0.7556 (tm-30) cc_final: 0.7285 (tm-30) REVERT: L 33 PHE cc_start: 0.8976 (t80) cc_final: 0.8673 (t80) REVERT: L 92 SER cc_start: 0.7841 (t) cc_final: 0.7592 (t) REVERT: L 206 ARG cc_start: 0.5250 (ttm-80) cc_final: 0.4908 (ttm110) REVERT: L 730 ASP cc_start: 0.8224 (t0) cc_final: 0.7578 (t70) REVERT: L 803 LEU cc_start: 0.6673 (OUTLIER) cc_final: 0.6323 (mt) REVERT: P 160 LEU cc_start: 0.7925 (tt) cc_final: 0.7429 (mp) outliers start: 38 outliers final: 32 residues processed: 206 average time/residue: 0.1937 time to fit residues: 57.6029 Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 178 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 534 THR Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 86 optimal weight: 0.0870 chunk 121 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 88 optimal weight: 1.9990 chunk 108 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 115 optimal weight: 0.5980 chunk 65 optimal weight: 5.9990 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 204 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 = 0.3968 r_free = 0.3968 target = 0.177982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.155908 restraints weight = 41192.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.160739 restraints weight = 19157.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.163689 restraints weight = 11349.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.165562 restraints weight = 7931.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.166744 restraints weight = 6213.583| |-----------------------------------------------------------------------------| r_work (final): 0.3826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 0.4515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10371 Z= 0.136 Angle : 0.603 6.362 14093 Z= 0.311 Chirality : 0.044 0.144 1570 Planarity : 0.004 0.046 1827 Dihedral : 7.450 81.270 1439 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.10 % Allowed : 16.79 % Favored : 80.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.83 (0.23), residues: 1266 helix: -0.29 (0.39), residues: 174 sheet: -0.87 (0.27), residues: 357 loop : -1.65 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 468 TYR 0.011 0.001 TYR L 626 PHE 0.017 0.002 PHE I 322 TRP 0.015 0.001 TRP I 298 HIS 0.014 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.14 (10371) covalent geometry : angle 0.60294 / 0.31 (14093) hydrogen bonds : bond 0.03866 / 2.53 ( 315) hydrogen bonds : angle 6.17313 / 4.40 ( 879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 181 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 20 GLN cc_start: 0.7568 (tm-30) cc_final: 0.7348 (tm-30) REVERT: L 33 PHE cc_start: 0.8944 (t80) cc_final: 0.8608 (t80) REVERT: L 92 SER cc_start: 0.7751 (t) cc_final: 0.7510 (t) REVERT: L 711 GLU cc_start: 0.6574 (tt0) cc_final: 0.6079 (tt0) REVERT: L 730 ASP cc_start: 0.8165 (t0) cc_final: 0.7590 (t70) REVERT: L 803 LEU cc_start: 0.6675 (OUTLIER) cc_final: 0.6349 (mt) REVERT: P 160 LEU cc_start: 0.7948 (tt) cc_final: 0.7459 (mp) REVERT: P 216 LEU cc_start: 0.7288 (OUTLIER) cc_final: 0.7039 (mp) outliers start: 34 outliers final: 27 residues processed: 201 average time/residue: 0.1665 time to fit residues: 50.0290 Evaluate side-chains 206 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 177 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 223 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 68 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 61.7869 > 50:) chunk 127 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 60 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 59 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 204 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 = 0.3928 r_free = 0.3928 target = 0.174514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.152187 restraints weight = 41477.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.156947 restraints weight = 19548.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.159948 restraints weight = 11673.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.161598 restraints weight = 8202.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 50)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162895 restraints weight = 6585.865| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.4667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10371 Z= 0.179 Angle : 0.625 5.371 14093 Z= 0.324 Chirality : 0.044 0.140 1570 Planarity : 0.005 0.045 1827 Dihedral : 7.505 82.693 1439 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer: Outliers : 3.56 % Allowed : 17.34 % Favored : 79.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.23), residues: 1266 helix: -0.30 (0.40), residues: 168 sheet: -0.99 (0.27), residues: 360 loop : -1.75 (0.22), residues: 738 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 858 TYR 0.017 0.002 TYR L 261 PHE 0.018 0.002 PHE L 621 TRP 0.016 0.002 TRP I 298 HIS 0.009 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.18 (10371) covalent geometry : angle 0.62528 / 0.32 (14093) hydrogen bonds : bond 0.04144 / 2.71 ( 315) hydrogen bonds : angle 6.25488 / 4.46 ( 879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 185 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 PHE cc_start: 0.8984 (t80) cc_final: 0.8656 (t80) REVERT: L 92 SER cc_start: 0.7845 (t) cc_final: 0.7618 (t) REVERT: L 730 ASP cc_start: 0.8267 (t0) cc_final: 0.7645 (t70) REVERT: L 803 LEU cc_start: 0.6694 (OUTLIER) cc_final: 0.6349 (mt) REVERT: P 160 LEU cc_start: 0.7987 (tt) cc_final: 0.7497 (mp) REVERT: P 216 LEU cc_start: 0.7272 (OUTLIER) cc_final: 0.7046 (mp) outliers start: 39 outliers final: 35 residues processed: 210 average time/residue: 0.1962 time to fit residues: 59.6675 Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 181 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 243 LEU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 453 GLU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 76 optimal weight: 0.1980 chunk 120 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 115 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 111 optimal weight: 0.0870 chunk 42 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 overall best weight: 1.6564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 418 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.175403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.153440 restraints weight = 41442.557| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.158164 restraints weight = 19368.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.161093 restraints weight = 11537.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.162963 restraints weight = 8110.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.163972 restraints weight = 6384.145| |-----------------------------------------------------------------------------| r_work (final): 0.3799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7136 moved from start: 0.4792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10371 Z= 0.173 Angle : 0.624 5.636 14093 Z= 0.323 Chirality : 0.045 0.164 1570 Planarity : 0.005 0.047 1827 Dihedral : 7.495 81.700 1439 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.65 % Allowed : 17.79 % Favored : 78.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.04 (0.23), residues: 1266 helix: -0.43 (0.39), residues: 174 sheet: -1.03 (0.27), residues: 357 loop : -1.78 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG P 157 TYR 0.015 0.002 TYR L 261 PHE 0.016 0.002 PHE L 621 TRP 0.016 0.002 TRP I 298 HIS 0.008 0.001 HIS L 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.17 (10371) covalent geometry : angle 0.62387 / 0.32 (14093) hydrogen bonds : bond 0.04103 / 2.67 ( 315) hydrogen bonds : angle 6.24279 / 4.44 ( 879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 175 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 PHE cc_start: 0.8992 (t80) cc_final: 0.8626 (t80) REVERT: L 92 SER cc_start: 0.7874 (t) cc_final: 0.7628 (t) REVERT: L 730 ASP cc_start: 0.8256 (t0) cc_final: 0.7624 (t70) REVERT: L 803 LEU cc_start: 0.6713 (OUTLIER) cc_final: 0.6370 (mt) REVERT: L 849 LEU cc_start: 0.7553 (tp) cc_final: 0.7209 (pt) REVERT: P 160 LEU cc_start: 0.7988 (tt) cc_final: 0.7481 (mp) REVERT: P 216 LEU cc_start: 0.7298 (OUTLIER) cc_final: 0.7060 (mp) outliers start: 40 outliers final: 35 residues processed: 198 average time/residue: 0.1838 time to fit residues: 54.4875 Evaluate side-chains 211 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 174 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 79 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 453 GLU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 47 optimal weight: 0.0980 chunk 1 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 120 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 29 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.0344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 354 HIS I 418 ASN ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.176442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.154259 restraints weight = 41294.927| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.159048 restraints weight = 19071.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.162038 restraints weight = 11292.514| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163912 restraints weight = 7901.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.164873 restraints weight = 6206.180| |-----------------------------------------------------------------------------| r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7105 moved from start: 0.4858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10371 Z= 0.133 Angle : 0.595 5.179 14093 Z= 0.306 Chirality : 0.044 0.159 1570 Planarity : 0.004 0.048 1827 Dihedral : 7.348 80.920 1439 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.87 % Favored : 93.13 % Rotamer: Outliers : 3.92 % Allowed : 17.79 % Favored : 78.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.86 (0.23), residues: 1266 helix: -0.27 (0.39), residues: 174 sheet: -0.91 (0.27), residues: 350 loop : -1.66 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG P 156 TYR 0.012 0.001 TYR L 626 PHE 0.015 0.002 PHE I 322 TRP 0.016 0.001 TRP I 298 HIS 0.008 0.001 HIS L 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (10371) covalent geometry : angle 0.59464 / 0.31 (14093) hydrogen bonds : bond 0.03776 / 2.47 ( 315) hydrogen bonds : angle 6.09907 / 4.34 ( 879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2532 Ramachandran restraints generated. 1266 Oldfield, 0 Emsley, 1266 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 175 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 33 PHE cc_start: 0.8965 (t80) cc_final: 0.8552 (t80) REVERT: L 92 SER cc_start: 0.7811 (t) cc_final: 0.7583 (t) REVERT: L 730 ASP cc_start: 0.8255 (t0) cc_final: 0.7629 (t70) REVERT: L 803 LEU cc_start: 0.6682 (OUTLIER) cc_final: 0.6342 (mt) REVERT: L 849 LEU cc_start: 0.7568 (tp) cc_final: 0.7183 (pt) REVERT: P 160 LEU cc_start: 0.7978 (tt) cc_final: 0.7512 (mp) REVERT: P 216 LEU cc_start: 0.7269 (OUTLIER) cc_final: 0.7033 (mp) outliers start: 43 outliers final: 38 residues processed: 200 average time/residue: 0.2055 time to fit residues: 60.3060 Evaluate side-chains 212 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 172 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 354 HIS Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 450 ARG Chi-restraints excluded: chain I residue 551 ASN Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 HIS Chi-restraints excluded: chain L residue 113 LEU Chi-restraints excluded: chain L residue 161 PHE Chi-restraints excluded: chain L residue 185 VAL Chi-restraints excluded: chain L residue 198 VAL Chi-restraints excluded: chain L residue 202 GLN Chi-restraints excluded: chain L residue 205 LEU Chi-restraints excluded: chain L residue 243 LEU Chi-restraints excluded: chain L residue 252 VAL Chi-restraints excluded: chain L residue 254 SER Chi-restraints excluded: chain L residue 295 LEU Chi-restraints excluded: chain L residue 300 GLU Chi-restraints excluded: chain L residue 321 HIS Chi-restraints excluded: chain L residue 322 CYS Chi-restraints excluded: chain L residue 323 VAL Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 374 LEU Chi-restraints excluded: chain L residue 382 VAL Chi-restraints excluded: chain L residue 411 ARG Chi-restraints excluded: chain L residue 432 ILE Chi-restraints excluded: chain L residue 453 GLU Chi-restraints excluded: chain L residue 457 VAL Chi-restraints excluded: chain L residue 560 LEU Chi-restraints excluded: chain L residue 608 THR Chi-restraints excluded: chain L residue 660 LEU Chi-restraints excluded: chain L residue 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 216 LEU Chi-restraints excluded: chain P residue 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 8 optimal weight: 0.9990 chunk 95 optimal weight: 1.9990 chunk 44 optimal weight: 0.0050 chunk 41 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 30 optimal weight: 0.7980 chunk 109 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 26 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 overall best weight: 0.6796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 418 ASN ** I 551 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.177112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.154887 restraints weight = 41024.533| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.159730 restraints weight = 19014.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.162739 restraints weight = 11208.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.164619 restraints weight = 7826.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165793 restraints weight = 6138.020| |-----------------------------------------------------------------------------| r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7087 moved from start: 0.4885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10371 Z= 0.158 Angle : 0.812 44.638 14093 Z= 0.517 Chirality : 0.044 0.167 1570 Planarity : 0.005 0.090 1827 Dihedral : 7.341 81.025 1439 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 7.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.71 % Favored : 93.29 % Rotamer: Outliers : 3.74 % Allowed : 18.07 % Favored : 78.19 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.23), residues: 1266 helix: -0.24 (0.40), residues: 174 sheet: -0.90 (0.27), residues: 350 loop : -1.63 (0.22), residues: 742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 666 TYR 0.011 0.001 TYR L 626 PHE 0.017 0.001 PHE I 552 TRP 0.015 0.001 TRP I 298 HIS 0.125 0.003 HIS I 354 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.16 (10371) covalent geometry : angle 0.81169 / 0.52 (14093) hydrogen bonds : bond 0.03682 / 2.41 ( 315) hydrogen bonds : angle 6.07076 / 4.32 ( 879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3197.25 seconds wall clock time: 55 minutes 8.41 seconds (3308.41 seconds total)