Starting phenix.real_space_refine on Thu Jun 19 01:19:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_18877_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_18877.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_18877.map" model { file = "/net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_18877_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8r3y_18877/06_2025/8r3y_18877_trim.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 9.08, per 1000 atoms: 0.45 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: 4.78 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 1.77 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: 7.55 Time building geometry restraints manager: 5.90 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: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.340 Extract box with map and model: 0.740 Check model and map are aligned: 0.150 Set scattering table: 0.200 Process input model: 42.140 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6934 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (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 TRP 0.166 0.026 TRP L 610 HIS 0.014 0.003 HIS L 31 PHE 0.092 0.016 PHE I 322 TYR 0.192 0.021 TYR L 261 ARG 0.011 0.001 ARG L 858 Details of bonding type rmsd hydrogen bonds : bond 0.18374 ( 315) hydrogen bonds : angle 8.96636 ( 879) covalent geometry : bond 0.01324 (10371) covalent geometry : angle 1.98333 (14093) *********************** 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 : 1.692 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 282 MET cc_start: 0.7642 (ttp) cc_final: 0.7440 (ttp) REVERT: I 410 THR cc_start: 0.5724 (OUTLIER) cc_final: 0.5307 (t) REVERT: I 529 MET cc_start: 0.6240 (mtp) cc_final: 0.6016 (mtt) REVERT: L 92 SER cc_start: 0.7455 (t) cc_final: 0.7222 (t) REVERT: L 277 THR cc_start: 0.6159 (m) cc_final: 0.5936 (m) REVERT: L 326 LEU cc_start: 0.5536 (tp) cc_final: 0.5247 (tp) REVERT: L 730 ASP cc_start: 0.8146 (t0) cc_final: 0.7805 (t0) REVERT: L 743 MET cc_start: 0.7969 (tmt) cc_final: 0.7368 (tmt) outliers start: 33 outliers final: 17 residues processed: 303 average time/residue: 0.6352 time to fit residues: 263.3336 Evaluate side-chains 234 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 327 ARG 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 202 LEU 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 108 optimal weight: 0.8980 chunk 97 optimal weight: 0.9990 chunk 53 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 74 optimal weight: 0.8980 chunk 116 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3987 r_free = 0.3987 target = 0.179685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.155847 restraints weight = 40610.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.160903 restraints weight = 18674.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.164077 restraints weight = 11088.945| |-----------------------------------------------------------------------------| r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7002 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10371 Z= 0.173 Angle : 0.789 7.403 14093 Z= 0.415 Chirality : 0.047 0.191 1570 Planarity : 0.007 0.161 1827 Dihedral : 9.467 66.489 1465 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.37 % Favored : 94.55 % Rotamer: Outliers : 2.74 % Allowed : 12.86 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.44 (0.22), residues: 1266 helix: -0.17 (0.39), residues: 155 sheet: -0.57 (0.26), residues: 346 loop : -1.32 (0.21), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP I 298 HIS 0.008 0.002 HIS L 786 PHE 0.030 0.002 PHE I 552 TYR 0.024 0.002 TYR L 261 ARG 0.006 0.001 ARG I 377 Details of bonding type rmsd hydrogen bonds : bond 0.05667 ( 315) hydrogen bonds : angle 7.10846 ( 879) covalent geometry : bond 0.00389 (10371) covalent geometry : angle 0.78948 (14093) *********************** 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 237 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.806 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: I 267 LYS cc_start: 0.5559 (tttt) cc_final: 0.3888 (mptt) REVERT: I 282 MET cc_start: 0.7635 (ttp) cc_final: 0.7414 (ttp) REVERT: I 401 LYS cc_start: 0.3984 (OUTLIER) cc_final: 0.3724 (tppt) REVERT: I 487 VAL cc_start: 0.8224 (m) cc_final: 0.7931 (p) REVERT: L 92 SER cc_start: 0.7571 (t) cc_final: 0.7336 (t) REVERT: L 206 ARG cc_start: 0.5514 (ttm-80) cc_final: 0.4999 (ttm110) REVERT: L 326 LEU cc_start: 0.5731 (tp) cc_final: 0.5423 (tp) REVERT: L 386 TYR cc_start: 0.8087 (p90) cc_final: 0.7863 (p90) REVERT: L 743 MET cc_start: 0.7968 (tmt) cc_final: 0.7495 (tmt) REVERT: P 229 ASP cc_start: 0.4635 (OUTLIER) cc_final: 0.4418 (m-30) outliers start: 30 outliers final: 19 residues processed: 227 average time/residue: 0.6830 time to fit residues: 222.8992 Evaluate side-chains 214 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 193 time to evaluate : 2.165 ------------------------------------------------------------------------------- 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 125 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 45 optimal weight: 7.9990 chunk 6 optimal weight: 0.0670 chunk 124 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 61 optimal weight: 6.9990 chunk 20 optimal weight: 3.9990 overall best weight: 1.1924 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 336 ASN I 418 ASN L 80 GLN L 783 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.181432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.158438 restraints weight = 40388.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.163414 restraints weight = 18780.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.166578 restraints weight = 11199.240| |-----------------------------------------------------------------------------| r_work (final): 0.3828 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7055 moved from start: 0.3476 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10371 Z= 0.148 Angle : 0.660 6.751 14093 Z= 0.344 Chirality : 0.045 0.181 1570 Planarity : 0.005 0.044 1827 Dihedral : 8.207 71.656 1448 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.85 % Favored : 94.15 % Rotamer: Outliers : 2.37 % Allowed : 13.96 % Favored : 83.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.59 (0.22), residues: 1266 helix: -0.08 (0.40), residues: 161 sheet: -0.81 (0.25), residues: 379 loop : -1.42 (0.22), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 298 HIS 0.006 0.001 HIS P 155 PHE 0.016 0.002 PHE I 552 TYR 0.017 0.002 TYR L 261 ARG 0.005 0.000 ARG I 377 Details of bonding type rmsd hydrogen bonds : bond 0.04469 ( 315) hydrogen bonds : angle 6.43672 ( 879) covalent geometry : bond 0.00323 (10371) covalent geometry : angle 0.66005 (14093) *********************** 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 223 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 197 time to evaluate : 2.288 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: I 267 LYS cc_start: 0.5633 (tttt) cc_final: 0.4004 (mptt) REVERT: L 67 GLU cc_start: 0.6756 (mp0) cc_final: 0.6229 (mp0) REVERT: L 92 SER cc_start: 0.7597 (t) cc_final: 0.7365 (t) REVERT: L 326 LEU cc_start: 0.5822 (tp) cc_final: 0.5498 (tp) REVERT: L 626 TYR cc_start: 0.8543 (OUTLIER) cc_final: 0.8076 (p90) REVERT: L 730 ASP cc_start: 0.8182 (t0) cc_final: 0.7458 (t70) REVERT: L 818 ASP cc_start: 0.8105 (t0) cc_final: 0.7890 (t70) outliers start: 26 outliers final: 17 residues processed: 216 average time/residue: 0.7621 time to fit residues: 243.4208 Evaluate side-chains 201 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 183 time to evaluate : 1.708 ------------------------------------------------------------------------------- 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 425 LEU 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 321 HIS Chi-restraints excluded: chain L residue 338 SER Chi-restraints excluded: chain L residue 382 VAL 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 223 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 64 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 88 optimal weight: 0.6980 chunk 79 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 418 ASN L 204 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.177582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.154874 restraints weight = 41122.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.159811 restraints weight = 19614.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.162856 restraints weight = 11782.683| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7168 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 10371 Z= 0.214 Angle : 0.675 6.891 14093 Z= 0.353 Chirality : 0.046 0.151 1570 Planarity : 0.005 0.047 1827 Dihedral : 8.133 82.095 1442 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.19 % Allowed : 15.24 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1266 helix: -0.42 (0.39), residues: 167 sheet: -0.87 (0.26), residues: 368 loop : -1.66 (0.21), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 298 HIS 0.007 0.001 HIS I 312 PHE 0.019 0.002 PHE I 552 TYR 0.021 0.002 TYR L 261 ARG 0.006 0.000 ARG L 709 Details of bonding type rmsd hydrogen bonds : bond 0.04672 ( 315) hydrogen bonds : angle 6.47731 ( 879) covalent geometry : bond 0.00469 (10371) covalent geometry : angle 0.67455 (14093) *********************** 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 224 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 189 time to evaluate : 1.465 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: L 33 PHE cc_start: 0.8954 (t80) cc_final: 0.8652 (t80) REVERT: L 92 SER cc_start: 0.7755 (t) cc_final: 0.7520 (t) REVERT: L 626 TYR cc_start: 0.8682 (OUTLIER) cc_final: 0.8067 (p90) REVERT: L 730 ASP cc_start: 0.8250 (t0) cc_final: 0.7654 (t70) REVERT: L 803 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.6326 (mt) outliers start: 35 outliers final: 27 residues processed: 210 average time/residue: 0.4686 time to fit residues: 139.5177 Evaluate side-chains 205 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 176 time to evaluate : 1.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 279 ILE Chi-restraints excluded: chain I residue 335 VAL Chi-restraints excluded: chain I residue 410 THR Chi-restraints excluded: chain I residue 425 LEU 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 79 THR Chi-restraints excluded: chain L residue 100 HIS Chi-restraints excluded: chain L residue 112 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 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 453 GLU 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 803 LEU Chi-restraints excluded: chain L residue 889 VAL Chi-restraints excluded: chain P residue 223 VAL 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 87 optimal weight: 1.9990 chunk 111 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 105 optimal weight: 5.9990 chunk 103 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 113 optimal weight: 0.9990 chunk 79 optimal weight: 0.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 418 ASN ** L 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 80 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.178052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.155936 restraints weight = 40899.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.160750 restraints weight = 19238.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.163750 restraints weight = 11465.793| |-----------------------------------------------------------------------------| r_work (final): 0.3791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 10371 Z= 0.166 Angle : 0.631 6.760 14093 Z= 0.327 Chirality : 0.045 0.158 1570 Planarity : 0.005 0.045 1827 Dihedral : 7.986 81.558 1442 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 3.47 % Allowed : 16.06 % Favored : 80.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.86 (0.22), residues: 1266 helix: -0.50 (0.38), residues: 173 sheet: -0.89 (0.26), residues: 358 loop : -1.62 (0.22), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 298 HIS 0.007 0.001 HIS L 31 PHE 0.028 0.002 PHE I 322 TYR 0.016 0.002 TYR L 261 ARG 0.005 0.000 ARG L 247 Details of bonding type rmsd hydrogen bonds : bond 0.04306 ( 315) hydrogen bonds : angle 6.33023 ( 879) covalent geometry : bond 0.00371 (10371) covalent geometry : angle 0.63138 (14093) *********************** 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 222 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 1.876 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: 0.8940 (t80) cc_final: 0.8638 (t80) REVERT: L 92 SER cc_start: 0.7759 (t) cc_final: 0.7544 (t) REVERT: L 626 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.7892 (p90) REVERT: L 641 ASN cc_start: 0.7593 (p0) cc_final: 0.7376 (p0) REVERT: L 730 ASP cc_start: 0.8203 (t0) cc_final: 0.7552 (t70) REVERT: L 803 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6329 (mt) REVERT: P 160 LEU cc_start: 0.7959 (tt) cc_final: 0.7376 (mp) outliers start: 38 outliers final: 30 residues processed: 207 average time/residue: 0.5151 time to fit residues: 153.0972 Evaluate side-chains 215 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 183 time to evaluate : 1.698 ------------------------------------------------------------------------------- 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 425 LEU 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 90 LEU 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 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 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 751 SER Chi-restraints excluded: chain L residue 778 LEU Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 878 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 102 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 45 optimal weight: 7.9990 chunk 41 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 113 optimal weight: 0.5980 chunk 9 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 336 ASN ** L 31 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 = 0.3920 r_free = 0.3920 target = 0.173686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.151133 restraints weight = 41640.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.155927 restraints weight = 19855.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.158925 restraints weight = 11952.593| |-----------------------------------------------------------------------------| r_work (final): 0.3751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10371 Z= 0.211 Angle : 0.660 6.315 14093 Z= 0.344 Chirality : 0.045 0.147 1570 Planarity : 0.005 0.050 1827 Dihedral : 7.963 81.666 1442 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.58 % Favored : 92.42 % Rotamer: Outliers : 3.65 % Allowed : 16.51 % Favored : 79.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.22), residues: 1266 helix: -0.48 (0.39), residues: 167 sheet: -1.12 (0.26), residues: 367 loop : -1.80 (0.22), residues: 732 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 298 HIS 0.008 0.001 HIS L 31 PHE 0.020 0.002 PHE I 322 TYR 0.019 0.002 TYR L 261 ARG 0.004 0.001 ARG L 858 Details of bonding type rmsd hydrogen bonds : bond 0.04498 ( 315) hydrogen bonds : angle 6.42685 ( 879) covalent geometry : bond 0.00466 (10371) covalent geometry : angle 0.66026 (14093) *********************** 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 230 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 190 time to evaluate : 1.695 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: L 20 GLN cc_start: 0.7534 (tm-30) cc_final: 0.7282 (tm-30) REVERT: L 33 PHE cc_start: 0.8976 (t80) cc_final: 0.8636 (t80) REVERT: L 92 SER cc_start: 0.7848 (t) cc_final: 0.7591 (t) REVERT: L 730 ASP cc_start: 0.8215 (t0) cc_final: 0.7566 (t70) REVERT: L 803 LEU cc_start: 0.6636 (OUTLIER) cc_final: 0.6276 (mt) REVERT: P 160 LEU cc_start: 0.7930 (tt) cc_final: 0.7404 (mp) outliers start: 40 outliers final: 33 residues processed: 214 average time/residue: 0.4940 time to fit residues: 149.1691 Evaluate side-chains 218 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 184 time to evaluate : 1.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 425 LEU 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 321 HIS Chi-restraints excluded: chain L residue 322 CYS 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 778 LEU 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 50 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 82 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 69 optimal weight: 0.6980 chunk 115 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.177316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.155093 restraints weight = 41093.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.159929 restraints weight = 19182.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.162937 restraints weight = 11380.594| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10371 Z= 0.143 Angle : 0.612 5.440 14093 Z= 0.316 Chirality : 0.044 0.145 1570 Planarity : 0.005 0.045 1827 Dihedral : 7.567 80.221 1439 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 3.92 % Allowed : 17.06 % Favored : 79.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.23), residues: 1266 helix: -0.43 (0.39), residues: 174 sheet: -1.02 (0.26), residues: 361 loop : -1.69 (0.22), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 298 HIS 0.009 0.001 HIS L 31 PHE 0.017 0.002 PHE I 322 TYR 0.012 0.001 TYR L 626 ARG 0.003 0.000 ARG L 468 Details of bonding type rmsd hydrogen bonds : bond 0.03942 ( 315) hydrogen bonds : angle 6.20157 ( 879) covalent geometry : bond 0.00322 (10371) covalent geometry : angle 0.61227 (14093) *********************** 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 227 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 184 time to evaluate : 1.623 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: L 20 GLN cc_start: 0.7572 (tm-30) cc_final: 0.7224 (tm-30) REVERT: L 33 PHE cc_start: 0.8948 (t80) cc_final: 0.8650 (t80) REVERT: L 43 ASP cc_start: 0.7993 (OUTLIER) cc_final: 0.7631 (m-30) REVERT: L 92 SER cc_start: 0.7771 (t) cc_final: 0.7508 (t) REVERT: L 730 ASP cc_start: 0.8179 (t0) cc_final: 0.7520 (t70) REVERT: L 803 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6260 (mt) REVERT: P 160 LEU cc_start: 0.7950 (tt) cc_final: 0.7429 (mp) outliers start: 43 outliers final: 36 residues processed: 210 average time/residue: 0.4935 time to fit residues: 149.4557 Evaluate side-chains 220 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 182 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 425 LEU 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 43 ASP 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 200 SER 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 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 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 223 VAL Chi-restraints excluded: chain P residue 227 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 33 optimal weight: 0.0980 chunk 102 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 67 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 48 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 20 optimal weight: 0.2980 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 41 optimal weight: 0.7980 overall best weight: 0.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.179124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.156868 restraints weight = 41105.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.161739 restraints weight = 19017.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.164769 restraints weight = 11251.780| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.4674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10371 Z= 0.110 Angle : 0.581 5.263 14093 Z= 0.296 Chirality : 0.044 0.144 1570 Planarity : 0.004 0.045 1827 Dihedral : 7.274 78.455 1439 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 3.38 % Allowed : 17.88 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.23), residues: 1266 helix: -0.25 (0.39), residues: 174 sheet: -0.85 (0.27), residues: 351 loop : -1.46 (0.23), residues: 741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 298 HIS 0.010 0.001 HIS L 31 PHE 0.017 0.001 PHE I 322 TYR 0.009 0.001 TYR L 626 ARG 0.006 0.000 ARG L 468 Details of bonding type rmsd hydrogen bonds : bond 0.03509 ( 315) hydrogen bonds : angle 5.93813 ( 879) covalent geometry : bond 0.00249 (10371) covalent geometry : angle 0.58087 (14093) *********************** 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 216 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 179 time to evaluate : 2.563 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: L 20 GLN cc_start: 0.7583 (tm-30) cc_final: 0.7277 (tm-30) REVERT: L 33 PHE cc_start: 0.8947 (t80) cc_final: 0.8600 (t80) REVERT: L 43 ASP cc_start: 0.8103 (OUTLIER) cc_final: 0.7725 (m-30) REVERT: L 92 SER cc_start: 0.7712 (t) cc_final: 0.7446 (t) REVERT: L 711 GLU cc_start: 0.6605 (tt0) cc_final: 0.6035 (tt0) REVERT: L 730 ASP cc_start: 0.8144 (t0) cc_final: 0.7416 (t70) REVERT: L 803 LEU cc_start: 0.6622 (OUTLIER) cc_final: 0.6330 (mt) REVERT: P 160 LEU cc_start: 0.7936 (tt) cc_final: 0.7459 (mp) outliers start: 37 outliers final: 32 residues processed: 202 average time/residue: 0.7661 time to fit residues: 235.1702 Evaluate side-chains 209 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 175 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 425 LEU 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 43 ASP 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 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 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 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 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 58 optimal weight: 0.4980 chunk 50 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 83 optimal weight: 0.8980 chunk 88 optimal weight: 0.0980 chunk 113 optimal weight: 0.3980 chunk 124 optimal weight: 3.9990 chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 93 optimal weight: 4.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.179064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.156827 restraints weight = 40931.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.161669 restraints weight = 19111.401| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.164665 restraints weight = 11368.552| |-----------------------------------------------------------------------------| r_work (final): 0.3811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7102 moved from start: 0.4790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 10371 Z= 0.107 Angle : 0.572 5.011 14093 Z= 0.290 Chirality : 0.043 0.141 1570 Planarity : 0.004 0.045 1827 Dihedral : 6.966 77.714 1436 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.28 % Allowed : 18.25 % Favored : 78.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1266 helix: -0.08 (0.40), residues: 174 sheet: -0.81 (0.26), residues: 356 loop : -1.37 (0.23), residues: 736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 298 HIS 0.005 0.001 HIS L 391 PHE 0.016 0.001 PHE I 322 TYR 0.008 0.001 TYR I 376 ARG 0.005 0.000 ARG L 468 Details of bonding type rmsd hydrogen bonds : bond 0.03404 ( 315) hydrogen bonds : angle 5.79764 ( 879) covalent geometry : bond 0.00245 (10371) covalent geometry : angle 0.57180 (14093) *********************** 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: 36 poor density : 179 time to evaluate : 1.894 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: 0.7551 (tm-30) cc_final: 0.7252 (tm-30) REVERT: L 33 PHE cc_start: 0.8901 (t80) cc_final: 0.8468 (t80) REVERT: L 43 ASP cc_start: 0.8068 (OUTLIER) cc_final: 0.7708 (m-30) REVERT: L 92 SER cc_start: 0.7686 (t) cc_final: 0.7442 (t) REVERT: L 711 GLU cc_start: 0.6585 (tt0) cc_final: 0.6101 (tt0) REVERT: L 730 ASP cc_start: 0.8119 (t0) cc_final: 0.7399 (t70) REVERT: L 803 LEU cc_start: 0.6610 (OUTLIER) cc_final: 0.6333 (mt) REVERT: P 160 LEU cc_start: 0.7990 (tt) cc_final: 0.7528 (mp) outliers start: 36 outliers final: 34 residues processed: 199 average time/residue: 0.4806 time to fit residues: 138.4308 Evaluate side-chains 210 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 174 time to evaluate : 1.586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 413 PHE Chi-restraints excluded: chain I residue 425 LEU 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 43 ASP 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 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 367 GLU 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 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 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 70 optimal weight: 1.9990 chunk 115 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 48 optimal weight: 0.0040 chunk 68 optimal weight: 0.1980 chunk 94 optimal weight: 0.9990 chunk 109 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 0.5192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 418 ASN I 551 ASN ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 900 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.180932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.159227 restraints weight = 40838.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.164047 restraints weight = 19023.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.167008 restraints weight = 11240.121| |-----------------------------------------------------------------------------| r_work (final): 0.3850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7078 moved from start: 0.4878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 10371 Z= 0.106 Angle : 0.564 5.074 14093 Z= 0.287 Chirality : 0.043 0.140 1570 Planarity : 0.004 0.044 1827 Dihedral : 6.752 76.340 1436 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 3.19 % Allowed : 18.43 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1266 helix: 0.10 (0.41), residues: 174 sheet: -0.72 (0.27), residues: 358 loop : -1.30 (0.23), residues: 734 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP I 298 HIS 0.004 0.001 HIS I 312 PHE 0.020 0.001 PHE L 336 TYR 0.013 0.001 TYR L 901 ARG 0.003 0.000 ARG P 174 Details of bonding type rmsd hydrogen bonds : bond 0.03271 ( 315) hydrogen bonds : angle 5.65680 ( 879) covalent geometry : bond 0.00242 (10371) covalent geometry : angle 0.56417 (14093) ********************** 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 210 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 2.704 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 20 GLN cc_start: 0.7541 (tm-30) cc_final: 0.7262 (tm-30) REVERT: L 43 ASP cc_start: 0.8061 (OUTLIER) cc_final: 0.7699 (m-30) REVERT: L 92 SER cc_start: 0.7674 (t) cc_final: 0.7420 (t) REVERT: L 711 GLU cc_start: 0.6631 (tt0) cc_final: 0.6115 (tt0) REVERT: L 730 ASP cc_start: 0.8116 (t0) cc_final: 0.7469 (t70) REVERT: P 160 LEU cc_start: 0.8010 (tt) cc_final: 0.7565 (mp) outliers start: 35 outliers final: 30 residues processed: 195 average time/residue: 0.5151 time to fit residues: 143.9005 Evaluate side-chains 202 residues out of total 1096 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 171 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 425 LEU Chi-restraints excluded: chain I residue 447 MET Chi-restraints excluded: chain I residue 450 ARG Chi-restraints excluded: chain I residue 557 THR Chi-restraints excluded: chain I residue 584 TYR Chi-restraints excluded: chain L residue 43 ASP Chi-restraints excluded: chain L residue 100 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 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 411 ARG 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 751 SER Chi-restraints excluded: chain L residue 803 LEU Chi-restraints excluded: chain L residue 830 GLU Chi-restraints excluded: chain L residue 878 LEU Chi-restraints excluded: chain P residue 171 PHE Chi-restraints excluded: chain P residue 198 VAL Chi-restraints excluded: chain P residue 223 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 128 random chunks: chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 chunk 119 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 92 optimal weight: 0.0770 chunk 72 optimal weight: 0.8980 chunk 105 optimal weight: 4.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 900 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.180100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.158414 restraints weight = 40915.184| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.163252 restraints weight = 19128.628| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.166220 restraints weight = 11275.262| |-----------------------------------------------------------------------------| r_work (final): 0.3845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7088 moved from start: 0.4946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10371 Z= 0.112 Angle : 0.563 5.034 14093 Z= 0.285 Chirality : 0.043 0.139 1570 Planarity : 0.004 0.043 1827 Dihedral : 6.706 76.333 1436 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 3.01 % Allowed : 18.43 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.23), residues: 1266 helix: 0.12 (0.41), residues: 174 sheet: -0.67 (0.27), residues: 357 loop : -1.30 (0.23), residues: 735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP I 298 HIS 0.004 0.001 HIS I 312 PHE 0.017 0.001 PHE L 343 TYR 0.009 0.001 TYR L 626 ARG 0.003 0.000 ARG P 174 Details of bonding type rmsd hydrogen bonds : bond 0.03340 ( 315) hydrogen bonds : angle 5.61466 ( 879) covalent geometry : bond 0.00257 (10371) covalent geometry : angle 0.56254 (14093) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8024.17 seconds wall clock time: 146 minutes 14.51 seconds (8774.51 seconds total)