Starting phenix.real_space_refine on Thu Aug 6 00:52:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.map" model { file = "/net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vx1_43606/08_2026/8vx1_43606.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 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 6213 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: 5 Type Number sf(0) Gaussians P 41 5.49 5 S 34 5.16 5 C 4558 2.51 5 N 1285 2.21 5 O 1456 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7374 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 861, 6520 Classifications: {'peptide': 861} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 98} Link IDs: {'PTRANS': 34, 'TRANS': 826} Chain breaks: 1 Unresolved non-hydrogen bonds: 417 Unresolved non-hydrogen angles: 498 Unresolved non-hydrogen dihedrals: 348 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLU:plan': 23, 'GLN:plan1': 13, 'ARG:plan': 11, 'HIS:plan': 3, 'ASP:plan': 6, 'PHE:plan': 3, 'ASN:plan1': 3} Unresolved non-hydrogen planarities: 261 Chain: "C" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 518 Inner-chain residues flagged as termini: ['pdbres=" DA C 10 "'] Classifications: {'DNA': 27} Modifications used: {'5*END': 2} Link IDs: {'rna3p': 26} Unresolved chain link angles: 1 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 50 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 45 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {' DT:plan': 2, ' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 32 Chain: "B" Number of atoms: 336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 336 Classifications: {'DNA': 16} Link IDs: {'rna3p': 15} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {' DT:plan': 1} Unresolved non-hydrogen planarities: 9 Time building chain proxies: 1.50, per 1000 atoms: 0.20 Number of scatterers: 7374 At special positions: 0 Unit cell: (76.44, 105.84, 114.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 34 16.00 P 41 15.00 O 1456 8.00 N 1285 7.00 C 4558 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 315.2 milliseconds 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1630 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 7 sheets defined 53.4% alpha, 9.1% beta 6 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 0.77 Creating SS restraints... Processing helix chain 'A' and resid 61 through 82 removed outlier: 3.560A pdb=" N LYS A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG A 82 " --> pdb=" O LYS A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 103 removed outlier: 3.845A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 removed outlier: 4.029A pdb=" N LEU A 187 " --> pdb=" O ASP A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.777A pdb=" N PHE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 6.116A pdb=" N SER A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 Processing helix chain 'A' and resid 237 through 254 removed outlier: 4.505A pdb=" N THR A 243 " --> pdb=" O THR A 239 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLN A 244 " --> pdb=" O THR A 240 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 314 through 324 removed outlier: 3.511A pdb=" N LEU A 318 " --> pdb=" O THR A 314 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N SER A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 removed outlier: 3.637A pdb=" N ARG A 341 " --> pdb=" O ILE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 338 through 341' Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.626A pdb=" N ASP A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.818A pdb=" N SER A 377 " --> pdb=" O ALA A 373 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 408 Processing helix chain 'A' and resid 431 through 456 removed outlier: 3.637A pdb=" N ALA A 439 " --> pdb=" O GLU A 435 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 440 " --> pdb=" O GLU A 436 " (cutoff:3.500A) Proline residue: A 446 - end of helix removed outlier: 3.642A pdb=" N GLN A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 removed outlier: 3.570A pdb=" N VAL A 463 " --> pdb=" O SER A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.513A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.878A pdb=" N SER A 518 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 removed outlier: 3.678A pdb=" N VAL A 533 " --> pdb=" O MET A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 560 removed outlier: 3.971A pdb=" N THR A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ILE A 560 " --> pdb=" O ALA A 556 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 560' Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 618 through 625 Processing helix chain 'A' and resid 639 through 648 removed outlier: 3.692A pdb=" N LYS A 646 " --> pdb=" O CYS A 642 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 659 removed outlier: 3.524A pdb=" N ARG A 659 " --> pdb=" O PHE A 656 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.911A pdb=" N HIS A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LEU A 695 " --> pdb=" O LEU A 691 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 714 removed outlier: 3.557A pdb=" N MET A 707 " --> pdb=" O HIS A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 717 through 729 Processing helix chain 'A' and resid 740 through 752 removed outlier: 3.649A pdb=" N LYS A 752 " --> pdb=" O LYS A 748 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 775 removed outlier: 4.169A pdb=" N VAL A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ARG A 774 " --> pdb=" O LYS A 770 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLY A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 789 through 811 removed outlier: 3.672A pdb=" N GLY A 801 " --> pdb=" O HIS A 797 " (cutoff:3.500A) Processing helix chain 'A' and resid 829 through 841 removed outlier: 3.598A pdb=" N ILE A 833 " --> pdb=" O ASN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.707A pdb=" N VAL A 878 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU A 879 " --> pdb=" O VAL A 876 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 875 through 879' Processing helix chain 'A' and resid 908 through 915 removed outlier: 3.595A pdb=" N LEU A 912 " --> pdb=" O SER A 908 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N PHE A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.507A pdb=" N LEU A 947 " --> pdb=" O ARG A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 977 through 988 Processing sheet with id=AA1, first strand: chain 'A' and resid 299 through 301 removed outlier: 3.842A pdb=" N THR A 313 " --> pdb=" O GLN A 295 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP A 336 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N THR A 228 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N SER A 368 " --> pdb=" O THR A 228 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N ILE A 230 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 5.935A pdb=" N VAL A 396 " --> pdb=" O CYS A 613 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N HIS A 615 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N TYR A 398 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N VAL A 566 " --> pdb=" O HIS A 612 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N TYR A 614 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 568 " --> pdb=" O TYR A 614 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N ALA A 492 " --> pdb=" O VAL A 565 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE A 493 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.768A pdb=" N ALA A 552 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N VAL A 495 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ILE A 551 " --> pdb=" O ILE A 524 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 574 through 577 Processing sheet with id=AA4, first strand: chain 'A' and resid 845 through 847 Processing sheet with id=AA5, first strand: chain 'A' and resid 850 through 851 removed outlier: 3.506A pdb=" N ASN A 851 " --> pdb=" O MET A 858 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N MET A 858 " --> pdb=" O ASN A 851 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 861 through 863 removed outlier: 3.888A pdb=" N VAL A 861 " --> pdb=" O VAL A 869 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N LEU A 901 " --> pdb=" O VAL A 868 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N ALA A 870 " --> pdb=" O LEU A 901 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 920 through 921 314 hydrogen bonds defined for protein. 906 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 0.74 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 1994 1.33 - 1.45: 1394 1.45 - 1.57: 4082 1.57 - 1.69: 81 1.69 - 1.81: 53 Bond restraints: 7604 Sorted by residual: bond pdb=" C3' DG C 2 " pdb=" C2' DG C 2 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.40e+00 bond pdb=" C3' DG B 15 " pdb=" C2' DG B 15 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.22e+00 bond pdb=" C3' DG B 12 " pdb=" C2' DG B 12 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.31e+00 bond pdb=" C3' DG B 13 " pdb=" C2' DG B 13 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.93e+00 bond pdb=" C3' DG C 13 " pdb=" C2' DG C 13 " ideal model delta sigma weight residual 1.516 1.533 -0.017 8.00e-03 1.56e+04 4.73e+00 ... (remaining 7599 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.16: 10381 2.16 - 4.33: 129 4.33 - 6.49: 8 6.49 - 8.66: 2 8.66 - 10.82: 2 Bond angle restraints: 10522 Sorted by residual: angle pdb=" N3 DT C 25 " pdb=" C4 DT C 25 " pdb=" O4 DT C 25 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT B 9 " pdb=" C4 DT B 9 " pdb=" O4 DT B 9 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT C 22 " pdb=" C4 DT C 22 " pdb=" O4 DT C 22 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 angle pdb=" N3 DT C 19 " pdb=" C4 DT C 19 " pdb=" O4 DT C 19 " ideal model delta sigma weight residual 119.90 122.36 -2.46 6.00e-01 2.78e+00 1.68e+01 angle pdb=" N3 DT C 20 " pdb=" C4 DT C 20 " pdb=" O4 DT C 20 " ideal model delta sigma weight residual 119.90 122.35 -2.45 6.00e-01 2.78e+00 1.67e+01 ... (remaining 10517 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.63: 3598 17.63 - 35.26: 540 35.26 - 52.90: 212 52.90 - 70.53: 61 70.53 - 88.16: 7 Dihedral angle restraints: 4418 sinusoidal: 1901 harmonic: 2517 Sorted by residual: dihedral pdb=" CA ASP A 361 " pdb=" CB ASP A 361 " pdb=" CG ASP A 361 " pdb=" OD1 ASP A 361 " ideal model delta sinusoidal sigma weight residual -30.00 -89.72 59.72 1 2.00e+01 2.50e-03 1.19e+01 dihedral pdb=" N LYS A 517 " pdb=" CA LYS A 517 " pdb=" CB LYS A 517 " pdb=" CG LYS A 517 " ideal model delta sinusoidal sigma weight residual -180.00 -120.78 -59.22 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ASP A 918 " pdb=" CB ASP A 918 " pdb=" CG ASP A 918 " pdb=" OD1 ASP A 918 " ideal model delta sinusoidal sigma weight residual -30.00 -82.68 52.68 1 2.00e+01 2.50e-03 9.45e+00 ... (remaining 4415 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 944 0.043 - 0.087: 202 0.087 - 0.130: 75 0.130 - 0.173: 0 0.173 - 0.216: 1 Chirality restraints: 1222 Sorted by residual: chirality pdb=" CB ILE A 848 " pdb=" CA ILE A 848 " pdb=" CG1 ILE A 848 " pdb=" CG2 ILE A 848 " both_signs ideal model delta sigma weight residual False 2.64 2.86 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA ILE A 936 " pdb=" N ILE A 936 " pdb=" C ILE A 936 " pdb=" CB ILE A 936 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 chirality pdb=" CA ILE A 551 " pdb=" N ILE A 551 " pdb=" C ILE A 551 " pdb=" CB ILE A 551 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.77e-01 ... (remaining 1219 not shown) Planarity restraints: 1196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 689 " 0.024 5.00e-02 4.00e+02 3.67e-02 2.15e+00 pdb=" N PRO A 690 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 690 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 690 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 354 " -0.006 2.00e-02 2.50e+03 1.24e-02 1.55e+00 pdb=" CG ASP A 354 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP A 354 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 354 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 848 " -0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C ILE A 848 " 0.020 2.00e-02 2.50e+03 pdb=" O ILE A 848 " -0.008 2.00e-02 2.50e+03 pdb=" N ARG A 849 " -0.007 2.00e-02 2.50e+03 ... (remaining 1193 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1720 2.79 - 3.32: 6718 3.32 - 3.85: 11634 3.85 - 4.37: 13287 4.37 - 4.90: 22849 Nonbonded interactions: 56208 Sorted by model distance: nonbonded pdb=" OG1 THR A 392 " pdb=" O GLY A 606 " model vdw 2.267 3.040 nonbonded pdb=" N1 DG C 6 " pdb=" O6 DG C 11 " model vdw 2.365 3.120 nonbonded pdb=" O ASN A 430 " pdb=" N GLN A 432 " model vdw 2.368 3.120 nonbonded pdb=" OG SER A 594 " pdb=" OD1 ASN A 597 " model vdw 2.373 3.040 nonbonded pdb=" N ASP A 324 " pdb=" OD1 ASP A 324 " model vdw 2.399 3.120 ... (remaining 56203 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.400 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 7.730 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7604 Z= 0.238 Angle : 0.551 10.821 10522 Z= 0.383 Chirality : 0.040 0.216 1222 Planarity : 0.003 0.038 1196 Dihedral : 19.915 88.159 2788 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.65 % Favored : 92.88 % Rotamer: Outliers : 0.30 % Allowed : 30.19 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.08 (0.30), residues: 857 helix: 1.07 (0.25), residues: 417 sheet: 0.67 (0.55), residues: 119 loop : -1.57 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 943 TYR 0.006 0.001 TYR A 842 PHE 0.017 0.001 PHE A 729 TRP 0.007 0.001 TRP A 887 HIS 0.002 0.000 HIS A 612 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.24 ( 7604) covalent geometry : angle 0.55073 / 0.38 (10522) hydrogen bonds : bond 0.27530 / 19.46 ( 326) hydrogen bonds : angle 6.29132 / 4.48 ( 906) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.229 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.0584 time to fit residues: 6.0381 Evaluate side-chains 57 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 967 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.0870 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 0.0670 overall best weight: 0.4298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 225 HIS A 597 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.085876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.060883 restraints weight = 17281.397| |-----------------------------------------------------------------------------| r_work (start): 0.2865 rms_B_bonded: 3.18 r_work: 0.2694 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8889 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 7604 Z= 0.146 Angle : 0.556 9.285 10522 Z= 0.306 Chirality : 0.040 0.229 1222 Planarity : 0.003 0.034 1196 Dihedral : 19.174 88.835 1330 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.07 % Favored : 93.47 % Rotamer: Outliers : 2.39 % Allowed : 27.35 % Favored : 70.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.30), residues: 857 helix: 1.85 (0.25), residues: 421 sheet: 0.49 (0.53), residues: 124 loop : -1.64 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 943 TYR 0.009 0.001 TYR A 483 PHE 0.013 0.001 PHE A 729 TRP 0.006 0.001 TRP A 500 HIS 0.003 0.001 HIS A 507 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.15 ( 7604) covalent geometry : angle 0.55567 / 0.31 (10522) hydrogen bonds : bond 0.07363 / 5.13 ( 326) hydrogen bonds : angle 4.50958 / 3.20 ( 906) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 59 time to evaluate : 0.251 Fit side-chains REVERT: A 438 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8785 (mp0) REVERT: A 511 MET cc_start: 0.9537 (mmt) cc_final: 0.9258 (mmm) REVERT: A 911 CYS cc_start: 0.9431 (m) cc_final: 0.9196 (m) outliers start: 16 outliers final: 4 residues processed: 71 average time/residue: 0.0530 time to fit residues: 6.0217 Evaluate side-chains 61 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 56 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 892 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 0.6980 chunk 56 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 79 optimal weight: 0.8980 chunk 55 optimal weight: 0.5980 chunk 43 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.084856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.059260 restraints weight = 17142.278| |-----------------------------------------------------------------------------| r_work (start): 0.2867 rms_B_bonded: 3.19 r_work: 0.2695 rms_B_bonded: 4.17 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7604 Z= 0.117 Angle : 0.509 9.856 10522 Z= 0.274 Chirality : 0.039 0.269 1222 Planarity : 0.003 0.035 1196 Dihedral : 19.281 88.277 1328 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.77 % Favored : 92.77 % Rotamer: Outliers : 3.29 % Allowed : 26.61 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.30), residues: 857 helix: 2.11 (0.26), residues: 425 sheet: 0.50 (0.53), residues: 124 loop : -1.73 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 952 TYR 0.009 0.001 TYR A 842 PHE 0.008 0.001 PHE A 729 TRP 0.006 0.001 TRP A 887 HIS 0.005 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.12 ( 7604) covalent geometry : angle 0.50875 / 0.27 (10522) hydrogen bonds : bond 0.04437 / 3.12 ( 326) hydrogen bonds : angle 3.94924 / 2.79 ( 906) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 59 time to evaluate : 0.254 Fit side-chains REVERT: A 438 GLU cc_start: 0.9070 (OUTLIER) cc_final: 0.8608 (mp0) REVERT: A 511 MET cc_start: 0.9544 (mmt) cc_final: 0.9255 (mmm) REVERT: A 534 ASN cc_start: 0.8415 (m110) cc_final: 0.8167 (m110) REVERT: A 640 GLU cc_start: 0.8839 (pm20) cc_final: 0.8524 (tp30) REVERT: A 858 MET cc_start: 0.8543 (pmm) cc_final: 0.8003 (pmm) REVERT: A 911 CYS cc_start: 0.9434 (m) cc_final: 0.9213 (m) REVERT: A 960 GLN cc_start: 0.9092 (OUTLIER) cc_final: 0.8839 (tm-30) outliers start: 22 outliers final: 12 residues processed: 77 average time/residue: 0.0487 time to fit residues: 5.9851 Evaluate side-chains 72 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.277 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 72 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 18 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 78 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 290 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.081795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.056246 restraints weight = 17662.395| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 3.22 r_work: 0.2635 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8960 moved from start: 0.1763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 7604 Z= 0.210 Angle : 0.561 11.947 10522 Z= 0.297 Chirality : 0.041 0.281 1222 Planarity : 0.003 0.035 1196 Dihedral : 19.375 89.161 1328 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.35 % Allowed : 7.23 % Favored : 92.42 % Rotamer: Outliers : 4.48 % Allowed : 25.71 % Favored : 69.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.31), residues: 857 helix: 2.45 (0.26), residues: 422 sheet: 0.40 (0.53), residues: 123 loop : -1.75 (0.35), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 746 TYR 0.017 0.001 TYR A 842 PHE 0.009 0.001 PHE A 729 TRP 0.009 0.001 TRP A 887 HIS 0.006 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.21 ( 7604) covalent geometry : angle 0.56128 / 0.30 (10522) hydrogen bonds : bond 0.04871 / 3.45 ( 326) hydrogen bonds : angle 4.01301 / 2.84 ( 906) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 50 time to evaluate : 0.175 Fit side-chains REVERT: A 438 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8710 (mp0) REVERT: A 858 MET cc_start: 0.8595 (pmm) cc_final: 0.8099 (pmm) REVERT: A 911 CYS cc_start: 0.9426 (m) cc_final: 0.9161 (m) REVERT: A 960 GLN cc_start: 0.9088 (OUTLIER) cc_final: 0.8789 (tm-30) outliers start: 30 outliers final: 18 residues processed: 76 average time/residue: 0.0592 time to fit residues: 6.7638 Evaluate side-chains 71 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 51 time to evaluate : 0.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 240 THR Chi-restraints excluded: chain A residue 350 THR Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 814 SER Chi-restraints excluded: chain A residue 892 LEU Chi-restraints excluded: chain A residue 905 THR Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.0070 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 0.0870 chunk 60 optimal weight: 8.9990 chunk 47 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 76 optimal weight: 1.9990 chunk 5 optimal weight: 4.9990 overall best weight: 0.9980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.057512 restraints weight = 17381.482| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.21 r_work: 0.2662 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7604 Z= 0.127 Angle : 0.516 12.253 10522 Z= 0.274 Chirality : 0.040 0.284 1222 Planarity : 0.003 0.037 1196 Dihedral : 19.358 89.452 1328 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.53 % Favored : 93.12 % Rotamer: Outliers : 3.14 % Allowed : 26.91 % Favored : 69.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.31), residues: 857 helix: 2.45 (0.26), residues: 427 sheet: 0.40 (0.53), residues: 123 loop : -1.66 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.011 0.001 TYR A 842 PHE 0.010 0.001 PHE A 496 TRP 0.007 0.001 TRP A 887 HIS 0.005 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.13 ( 7604) covalent geometry : angle 0.51554 / 0.27 (10522) hydrogen bonds : bond 0.04051 / 2.88 ( 326) hydrogen bonds : angle 3.74827 / 2.65 ( 906) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.251 Fit side-chains REVERT: A 438 GLU cc_start: 0.9097 (OUTLIER) cc_final: 0.8693 (mp0) REVERT: A 640 GLU cc_start: 0.8832 (pm20) cc_final: 0.8507 (tp30) REVERT: A 858 MET cc_start: 0.8606 (pmm) cc_final: 0.8115 (pmm) REVERT: A 911 CYS cc_start: 0.9442 (m) cc_final: 0.9191 (m) REVERT: A 960 GLN cc_start: 0.9063 (OUTLIER) cc_final: 0.8775 (tm-30) outliers start: 21 outliers final: 14 residues processed: 72 average time/residue: 0.0539 time to fit residues: 6.0546 Evaluate side-chains 65 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 49 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.0170 chunk 8 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 77 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 8.9990 chunk 73 optimal weight: 3.9990 overall best weight: 0.6818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2816 r_free = 0.2816 target = 0.058106 restraints weight = 17316.767| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.24 r_work: 0.2683 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8915 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 7604 Z= 0.108 Angle : 0.499 13.023 10522 Z= 0.263 Chirality : 0.040 0.275 1222 Planarity : 0.003 0.037 1196 Dihedral : 19.369 89.194 1328 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.99 % Allowed : 26.91 % Favored : 70.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.31), residues: 857 helix: 2.52 (0.26), residues: 427 sheet: 0.41 (0.53), residues: 123 loop : -1.65 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.009 0.001 TYR A 842 PHE 0.006 0.001 PHE A 729 TRP 0.007 0.001 TRP A 887 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00216 / 0.11 ( 7604) covalent geometry : angle 0.49909 / 0.26 (10522) hydrogen bonds : bond 0.03630 / 2.57 ( 326) hydrogen bonds : angle 3.60664 / 2.56 ( 906) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.194 Fit side-chains REVERT: A 438 GLU cc_start: 0.9123 (OUTLIER) cc_final: 0.8836 (mp0) REVERT: A 534 ASN cc_start: 0.8430 (m110) cc_final: 0.8214 (m110) REVERT: A 858 MET cc_start: 0.8608 (pmm) cc_final: 0.8060 (pmm) REVERT: A 911 CYS cc_start: 0.9437 (m) cc_final: 0.9176 (m) REVERT: A 960 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8773 (tm-30) outliers start: 20 outliers final: 16 residues processed: 70 average time/residue: 0.0579 time to fit residues: 6.1877 Evaluate side-chains 71 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 46 optimal weight: 0.9990 chunk 49 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 84 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 59 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.083746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.058327 restraints weight = 17401.639| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.22 r_work: 0.2681 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8917 moved from start: 0.2009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7604 Z= 0.115 Angle : 0.510 12.255 10522 Z= 0.266 Chirality : 0.039 0.261 1222 Planarity : 0.003 0.038 1196 Dihedral : 19.380 89.282 1328 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.53 % Favored : 93.12 % Rotamer: Outliers : 2.99 % Allowed : 27.50 % Favored : 69.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.27 (0.31), residues: 857 helix: 2.59 (0.26), residues: 427 sheet: 0.42 (0.53), residues: 123 loop : -1.64 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.010 0.001 TYR A 842 PHE 0.005 0.001 PHE A 496 TRP 0.006 0.001 TRP A 887 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 7604) covalent geometry : angle 0.51009 / 0.27 (10522) hydrogen bonds : bond 0.03555 / 2.51 ( 326) hydrogen bonds : angle 3.58002 / 2.54 ( 906) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 55 time to evaluate : 0.223 Fit side-chains REVERT: A 438 GLU cc_start: 0.9129 (OUTLIER) cc_final: 0.8921 (mp0) REVERT: A 534 ASN cc_start: 0.8459 (m110) cc_final: 0.8219 (m110) REVERT: A 858 MET cc_start: 0.8618 (pmm) cc_final: 0.8066 (pmm) REVERT: A 911 CYS cc_start: 0.9428 (m) cc_final: 0.9159 (m) REVERT: A 960 GLN cc_start: 0.9065 (OUTLIER) cc_final: 0.8780 (tm-30) outliers start: 20 outliers final: 14 residues processed: 72 average time/residue: 0.0570 time to fit residues: 6.3070 Evaluate side-chains 70 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 54 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 438 GLU Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 54 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 0.4980 chunk 65 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 47 optimal weight: 6.9990 chunk 88 optimal weight: 20.0000 chunk 42 optimal weight: 0.9990 chunk 71 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.084085 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.058661 restraints weight = 17456.708| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.23 r_work: 0.2689 rms_B_bonded: 4.18 restraints_weight: 0.5000 r_work (final): 0.2689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8910 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 7604 Z= 0.106 Angle : 0.491 12.002 10522 Z= 0.259 Chirality : 0.040 0.266 1222 Planarity : 0.003 0.038 1196 Dihedral : 19.411 89.623 1328 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.67 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.77 % Favored : 92.88 % Rotamer: Outliers : 2.69 % Allowed : 28.10 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.30 (0.31), residues: 857 helix: 2.64 (0.26), residues: 426 sheet: 0.46 (0.53), residues: 123 loop : -1.65 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 297 TYR 0.009 0.001 TYR A 842 PHE 0.004 0.001 PHE A 496 TRP 0.007 0.001 TRP A 68 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00215 / 0.11 ( 7604) covalent geometry : angle 0.49075 / 0.26 (10522) hydrogen bonds : bond 0.03313 / 2.34 ( 326) hydrogen bonds : angle 3.48227 / 2.47 ( 906) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 56 time to evaluate : 0.234 Fit side-chains REVERT: A 534 ASN cc_start: 0.8427 (m110) cc_final: 0.8195 (m110) REVERT: A 640 GLU cc_start: 0.8802 (pm20) cc_final: 0.8487 (tp30) REVERT: A 960 GLN cc_start: 0.9043 (OUTLIER) cc_final: 0.8740 (tm-30) outliers start: 18 outliers final: 14 residues processed: 70 average time/residue: 0.0519 time to fit residues: 5.5545 Evaluate side-chains 69 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 960 GLN Chi-restraints excluded: chain A residue 963 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 17 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 78 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 73 optimal weight: 0.0770 chunk 67 optimal weight: 0.9990 chunk 50 optimal weight: 0.6980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.082877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.056950 restraints weight = 17195.724| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.39 r_work: 0.2609 rms_B_bonded: 4.31 restraints_weight: 0.5000 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7604 Z= 0.109 Angle : 0.515 12.528 10522 Z= 0.266 Chirality : 0.040 0.257 1222 Planarity : 0.003 0.039 1196 Dihedral : 19.406 89.921 1328 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.77 % Favored : 92.88 % Rotamer: Outliers : 2.39 % Allowed : 28.85 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.31), residues: 857 helix: 2.67 (0.26), residues: 426 sheet: 0.49 (0.53), residues: 123 loop : -1.64 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.009 0.001 TYR A 842 PHE 0.004 0.001 PHE A 729 TRP 0.007 0.001 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 7604) covalent geometry : angle 0.51520 / 0.27 (10522) hydrogen bonds : bond 0.03224 / 2.27 ( 326) hydrogen bonds : angle 3.45924 / 2.46 ( 906) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 55 time to evaluate : 0.235 Fit side-chains REVERT: A 534 ASN cc_start: 0.8415 (m110) cc_final: 0.8190 (m110) outliers start: 16 outliers final: 13 residues processed: 68 average time/residue: 0.0554 time to fit residues: 5.8826 Evaluate side-chains 67 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 886 ASN Chi-restraints excluded: chain A residue 908 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 39 optimal weight: 0.8980 chunk 26 optimal weight: 0.5980 chunk 88 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 84 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 15 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 overall best weight: 0.6118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.083770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.058475 restraints weight = 17108.482| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 3.28 r_work: 0.2621 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7604 Z= 0.103 Angle : 0.501 11.024 10522 Z= 0.262 Chirality : 0.039 0.215 1222 Planarity : 0.003 0.039 1196 Dihedral : 19.400 89.683 1328 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.88 % Favored : 92.77 % Rotamer: Outliers : 2.09 % Allowed : 28.70 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.37 (0.31), residues: 857 helix: 2.68 (0.26), residues: 427 sheet: 0.56 (0.53), residues: 123 loop : -1.64 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 849 TYR 0.009 0.001 TYR A 842 PHE 0.004 0.001 PHE A 729 TRP 0.007 0.001 TRP A 68 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00210 / 0.10 ( 7604) covalent geometry : angle 0.50060 / 0.26 (10522) hydrogen bonds : bond 0.03122 / 2.20 ( 326) hydrogen bonds : angle 3.42533 / 2.44 ( 906) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1714 Ramachandran restraints generated. 857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 55 time to evaluate : 0.210 Fit side-chains REVERT: A 534 ASN cc_start: 0.8393 (m110) cc_final: 0.8169 (m110) REVERT: A 640 GLU cc_start: 0.8831 (pm20) cc_final: 0.8412 (tp30) outliers start: 14 outliers final: 14 residues processed: 67 average time/residue: 0.0537 time to fit residues: 5.5606 Evaluate side-chains 68 residues out of total 771 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 105 VAL Chi-restraints excluded: chain A residue 364 VAL Chi-restraints excluded: chain A residue 486 LEU Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 581 THR Chi-restraints excluded: chain A residue 618 ASN Chi-restraints excluded: chain A residue 619 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 707 MET Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 886 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 83 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 86 optimal weight: 30.0000 chunk 40 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 42 optimal weight: 0.0980 chunk 58 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.082757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.056746 restraints weight = 17218.111| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.40 r_work: 0.2604 rms_B_bonded: 4.32 restraints_weight: 0.5000 r_work (final): 0.2604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 7604 Z= 0.121 Angle : 0.507 10.671 10522 Z= 0.264 Chirality : 0.040 0.373 1222 Planarity : 0.003 0.039 1196 Dihedral : 19.409 89.379 1328 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.35 % Allowed : 6.53 % Favored : 93.12 % Rotamer: Outliers : 2.39 % Allowed : 28.40 % Favored : 69.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.31), residues: 857 helix: 2.67 (0.26), residues: 427 sheet: 0.53 (0.53), residues: 123 loop : -1.64 (0.36), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 297 TYR 0.010 0.001 TYR A 842 PHE 0.004 0.001 PHE A 376 TRP 0.008 0.001 TRP A 68 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 7604) covalent geometry : angle 0.50707 / 0.26 (10522) hydrogen bonds : bond 0.03292 / 2.31 ( 326) hydrogen bonds : angle 3.50311 / 2.51 ( 906) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1283.73 seconds wall clock time: 22 minutes 37.23 seconds (1357.23 seconds total)