Starting phenix.real_space_refine on Fri Jul 3 05:27:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vx8_43612/07_2026/8vx8_43612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vx8_43612/07_2026/8vx8_43612.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/8vx8_43612/07_2026/8vx8_43612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vx8_43612/07_2026/8vx8_43612.map" model { file = "/net/cci-nas-00/data/ceres_data/8vx8_43612/07_2026/8vx8_43612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vx8_43612/07_2026/8vx8_43612.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= 0.016 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 6143 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 34 5.49 5 S 34 5.16 5 C 4436 2.51 5 N 1249 2.21 5 O 1399 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 7152 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 843, 6401 Classifications: {'peptide': 843} Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 90} Link IDs: {'PTRANS': 34, 'TRANS': 808} Chain breaks: 2 Unresolved non-hydrogen bonds: 380 Unresolved non-hydrogen angles: 449 Unresolved non-hydrogen dihedrals: 315 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'ARG:plan': 10, 'GLU:plan': 26, 'GLN:plan1': 9, 'HIS:plan': 1, 'ASP:plan': 6, 'ASN:plan1': 3, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 230 Chain: "B" Number of atoms: 470 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 470 Inner-chain residues flagged as termini: ['pdbres=" DT B 5 "', 'pdbres=" DA B 10 "', 'pdbres=" DT B 14 "'] Classifications: {'DNA': 26} Modifications used: {'5*END': 4} Link IDs: {'rna3p': 25} Unresolved chain link angles: 4 Unresolved chain link dihedrals: 8 Unresolved non-hydrogen bonds: 76 Unresolved non-hydrogen angles: 110 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {' DA%5*END:plan': 2, ' DA%5*END:plan2': 2, ' DT%5*END:plan': 2} Unresolved non-hydrogen planarities: 46 Chain: "C" Number of atoms: 281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 281 Inner-chain residues flagged as termini: ['pdbres=" DT C 5 "', 'pdbres=" DA C 10 "'] Classifications: {'DNA': 15} Modifications used: {'5*END': 3} Link IDs: {'rna3p': 14} Unresolved chain link angles: 2 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 58 Unresolved non-hydrogen dihedrals: 38 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' DT%5*END:plan': 1, ' DA%5*END:plan': 1, ' DA%5*END:plan2': 1} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 1.64, per 1000 atoms: 0.23 Number of scatterers: 7152 At special positions: 0 Unit cell: (76.44, 105, 110.04, 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 34 15.00 O 1399 8.00 N 1249 7.00 C 4436 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: 0.47 Conformation dependent library (CDL) restraints added in 346.2 milliseconds 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 6 sheets defined 54.3% alpha, 9.3% beta 6 base pairs and 18 stacking pairs defined. Time for finding SS restraints: 0.90 Creating SS restraints... Processing helix chain 'A' and resid 63 through 83 removed outlier: 3.772A pdb=" N GLN A 83 " --> pdb=" O GLU A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 removed outlier: 3.571A pdb=" N GLU A 96 " --> pdb=" O GLU A 92 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 196 through 207 removed outlier: 3.516A pdb=" N PHE A 205 " --> pdb=" O GLU A 201 " (cutoff:3.500A) Processing helix chain 'A' and resid 208 through 213 removed outlier: 6.139A pdb=" N SER A 211 " --> pdb=" O LYS A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 225 removed outlier: 3.692A pdb=" N ASN A 220 " --> pdb=" O LYS A 216 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 254 removed outlier: 3.556A pdb=" N GLY A 254 " --> pdb=" O TYR A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 282 Processing helix chain 'A' and resid 314 through 324 removed outlier: 4.175A pdb=" N GLN A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER A 323 " --> pdb=" O GLN A 319 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ASP A 324 " --> pdb=" O TRP A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 341 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.647A pdb=" N ASP A 346 " --> pdb=" O ASN A 342 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N VAL A 347 " --> pdb=" O LEU A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 380 removed outlier: 3.873A 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 432 through 444 Processing helix chain 'A' and resid 444 through 456 removed outlier: 5.002A pdb=" N GLN A 454 " --> pdb=" O ARG A 450 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ARG A 455 " --> pdb=" O GLU A 451 " (cutoff:3.500A) Processing helix chain 'A' and resid 457 through 466 Processing helix chain 'A' and resid 473 through 487 removed outlier: 3.776A pdb=" N ILE A 477 " --> pdb=" O ASP A 473 " (cutoff:3.500A) Processing helix chain 'A' and resid 499 through 513 removed outlier: 3.834A pdb=" N THR A 505 " --> pdb=" O ASP A 501 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLN A 513 " --> pdb=" O LEU A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.794A pdb=" N SER A 518 " --> pdb=" O MET A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 535 Processing helix chain 'A' and resid 554 through 559 removed outlier: 3.770A pdb=" N THR A 558 " --> pdb=" O ASN A 554 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N SER A 559 " --> pdb=" O ILE A 555 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 554 through 559' Processing helix chain 'A' and resid 594 through 603 Processing helix chain 'A' and resid 618 through 624 Processing helix chain 'A' and resid 631 through 635 Processing helix chain 'A' and resid 639 through 648 Processing helix chain 'A' and resid 655 through 659 Processing helix chain 'A' and resid 665 through 679 Processing helix chain 'A' and resid 689 through 698 removed outlier: 3.760A pdb=" N HIS A 694 " --> pdb=" O PRO A 690 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 714 Processing helix chain 'A' and resid 716 through 729 removed outlier: 3.548A pdb=" N VAL A 720 " --> pdb=" O CYS A 716 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 752 removed outlier: 3.578A pdb=" N GLU A 749 " --> pdb=" O ALA A 745 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 750 " --> pdb=" O ARG A 746 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 773 removed outlier: 4.072A pdb=" N VAL A 761 " --> pdb=" O ASP A 757 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N VAL A 762 " --> pdb=" O HIS A 758 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLN A 773 " --> pdb=" O GLU A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 775 through 786 Processing helix chain 'A' and resid 789 through 811 Processing helix chain 'A' and resid 829 through 841 removed outlier: 3.538A pdb=" N ILE A 833 " --> pdb=" O ASN A 829 " (cutoff:3.500A) Processing helix chain 'A' and resid 875 through 879 removed outlier: 3.675A pdb=" N VAL A 878 " --> pdb=" O SER A 875 " (cutoff:3.500A) removed outlier: 4.326A 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: 3.524A pdb=" N PHE A 914 " --> pdb=" O TYR A 910 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 915 " --> pdb=" O CYS A 911 " (cutoff:3.500A) Processing helix chain 'A' and resid 941 through 965 removed outlier: 3.907A 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: 6.881A pdb=" N GLY A 293 " --> pdb=" O TYR A 311 " (cutoff:3.500A) removed outlier: 9.029A pdb=" N THR A 313 " --> pdb=" O GLY A 293 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N GLN A 295 " --> pdb=" O THR A 313 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N ILE A 261 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N CYS A 312 " --> pdb=" O ILE A 261 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N CYS A 263 " --> pdb=" O CYS A 312 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL A 262 " --> pdb=" O VAL A 334 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ASP A 336 " --> pdb=" O VAL A 262 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N THR A 264 " --> pdb=" O ASP A 336 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 228 " --> pdb=" O VAL A 364 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N GLY A 232 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 395 through 398 removed outlier: 3.631A pdb=" N VAL A 396 " --> pdb=" O GLY A 611 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N LEU A 494 " --> pdb=" O ILE A 569 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ILE A 493 " --> pdb=" O VAL A 550 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N ALA A 552 " --> pdb=" O ILE A 493 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N VAL A 495 " --> pdb=" O ALA A 552 " (cutoff:3.500A) removed outlier: 3.562A 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 576 Processing sheet with id=AA4, first strand: chain 'A' and resid 586 through 587 removed outlier: 6.926A pdb=" N SER A 586 " --> pdb=" O ARG A 895 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 858 through 862 removed outlier: 4.055A pdb=" N MET A 858 " --> pdb=" O ASN A 851 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 920 through 921 318 hydrogen bonds defined for protein. 903 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 12 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 6 basepair parallelities 18 stacking parallelities Total time for adding SS restraints: 1.59 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1265 1.33 - 1.45: 1950 1.45 - 1.57: 4029 1.57 - 1.69: 68 1.69 - 1.81: 53 Bond restraints: 7365 Sorted by residual: bond pdb=" C5' DG C 17 " pdb=" C4' DG C 17 " ideal model delta sigma weight residual 1.512 1.542 -0.030 7.00e-03 2.04e+04 1.86e+01 bond pdb=" C6 DG B 13 " pdb=" N1 DG B 13 " ideal model delta sigma weight residual 1.391 1.421 -0.030 7.00e-03 2.04e+04 1.82e+01 bond pdb=" C5' DG B 17 " pdb=" C4' DG B 17 " ideal model delta sigma weight residual 1.512 1.541 -0.029 7.00e-03 2.04e+04 1.71e+01 bond pdb=" C5' DG B 8 " pdb=" C4' DG B 8 " ideal model delta sigma weight residual 1.512 1.539 -0.027 7.00e-03 2.04e+04 1.47e+01 bond pdb=" C6 DG B 8 " pdb=" N1 DG B 8 " ideal model delta sigma weight residual 1.391 1.418 -0.027 7.00e-03 2.04e+04 1.46e+01 ... (remaining 7360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 9799 2.00 - 3.99: 277 3.99 - 5.99: 63 5.99 - 7.98: 30 7.98 - 9.98: 8 Bond angle restraints: 10177 Sorted by residual: angle pdb=" O5' DG B 8 " pdb=" C5' DG B 8 " pdb=" C4' DG B 8 " ideal model delta sigma weight residual 109.40 115.22 -5.82 8.00e-01 1.56e+00 5.30e+01 angle pdb=" O5' DG C 17 " pdb=" C5' DG C 17 " pdb=" C4' DG C 17 " ideal model delta sigma weight residual 109.40 114.80 -5.40 8.00e-01 1.56e+00 4.56e+01 angle pdb=" O5' DG B 17 " pdb=" C5' DG B 17 " pdb=" C4' DG B 17 " ideal model delta sigma weight residual 109.40 114.76 -5.36 8.00e-01 1.56e+00 4.48e+01 angle pdb=" CA ARG A 635 " pdb=" C ARG A 635 " pdb=" N THR A 636 " ideal model delta sigma weight residual 115.75 124.24 -8.49 1.34e+00 5.57e-01 4.01e+01 angle pdb=" N ARG A 635 " pdb=" CA ARG A 635 " pdb=" C ARG A 635 " ideal model delta sigma weight residual 109.65 100.85 8.80 1.56e+00 4.11e-01 3.18e+01 ... (remaining 10172 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 3483 17.39 - 34.79: 500 34.79 - 52.18: 215 52.18 - 69.57: 60 69.57 - 86.96: 8 Dihedral angle restraints: 4266 sinusoidal: 1800 harmonic: 2466 Sorted by residual: dihedral pdb=" CA SER A 559 " pdb=" C SER A 559 " pdb=" N ILE A 560 " pdb=" CA ILE A 560 " ideal model delta harmonic sigma weight residual 180.00 163.21 16.79 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA CYS A 716 " pdb=" C CYS A 716 " pdb=" N LEU A 717 " pdb=" CA LEU A 717 " ideal model delta harmonic sigma weight residual -180.00 -163.99 -16.01 0 5.00e+00 4.00e-02 1.03e+01 dihedral pdb=" CB GLU A 805 " pdb=" CG GLU A 805 " pdb=" CD GLU A 805 " pdb=" OE1 GLU A 805 " ideal model delta sinusoidal sigma weight residual 0.00 -84.82 84.82 1 3.00e+01 1.11e-03 9.70e+00 ... (remaining 4263 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.123: 1144 0.123 - 0.246: 18 0.246 - 0.369: 0 0.369 - 0.491: 2 0.491 - 0.614: 19 Chirality restraints: 1183 Sorted by residual: chirality pdb=" P DG C 7 " pdb=" OP1 DG C 7 " pdb=" OP2 DG C 7 " pdb=" O5' DG C 7 " both_signs ideal model delta sigma weight residual True 2.34 -2.95 -0.61 2.00e-01 2.50e+01 9.43e+00 chirality pdb=" P DG C 8 " pdb=" OP1 DG C 8 " pdb=" OP2 DG C 8 " pdb=" O5' DG C 8 " both_signs ideal model delta sigma weight residual True 2.34 -2.93 -0.59 2.00e-01 2.50e+01 8.73e+00 chirality pdb=" P DG C 13 " pdb=" OP1 DG C 13 " pdb=" OP2 DG C 13 " pdb=" O5' DG C 13 " both_signs ideal model delta sigma weight residual True 2.34 -2.92 -0.59 2.00e-01 2.50e+01 8.68e+00 ... (remaining 1180 not shown) Planarity restraints: 1170 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG B 4 " 0.174 2.00e-02 2.50e+03 7.26e-02 1.58e+02 pdb=" N9 DG B 4 " -0.052 2.00e-02 2.50e+03 pdb=" C8 DG B 4 " -0.016 2.00e-02 2.50e+03 pdb=" N7 DG B 4 " -0.051 2.00e-02 2.50e+03 pdb=" C5 DG B 4 " -0.072 2.00e-02 2.50e+03 pdb=" C6 DG B 4 " 0.019 2.00e-02 2.50e+03 pdb=" O6 DG B 4 " 0.123 2.00e-02 2.50e+03 pdb=" N1 DG B 4 " 0.008 2.00e-02 2.50e+03 pdb=" C2 DG B 4 " -0.019 2.00e-02 2.50e+03 pdb=" N2 DG B 4 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DG B 4 " -0.047 2.00e-02 2.50e+03 pdb=" C4 DG B 4 " -0.065 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG C 17 " 0.118 2.00e-02 2.50e+03 5.26e-02 8.29e+01 pdb=" N9 DG C 17 " -0.017 2.00e-02 2.50e+03 pdb=" C8 DG C 17 " -0.069 2.00e-02 2.50e+03 pdb=" N7 DG C 17 " -0.061 2.00e-02 2.50e+03 pdb=" C5 DG C 17 " -0.016 2.00e-02 2.50e+03 pdb=" C6 DG C 17 " 0.036 2.00e-02 2.50e+03 pdb=" O6 DG C 17 " 0.060 2.00e-02 2.50e+03 pdb=" N1 DG C 17 " 0.036 2.00e-02 2.50e+03 pdb=" C2 DG C 17 " -0.006 2.00e-02 2.50e+03 pdb=" N2 DG C 17 " -0.060 2.00e-02 2.50e+03 pdb=" N3 DG C 17 " -0.022 2.00e-02 2.50e+03 pdb=" C4 DG C 17 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG B 17 " -0.117 2.00e-02 2.50e+03 5.25e-02 8.27e+01 pdb=" N9 DG B 17 " 0.017 2.00e-02 2.50e+03 pdb=" C8 DG B 17 " 0.068 2.00e-02 2.50e+03 pdb=" N7 DG B 17 " 0.062 2.00e-02 2.50e+03 pdb=" C5 DG B 17 " 0.015 2.00e-02 2.50e+03 pdb=" C6 DG B 17 " -0.035 2.00e-02 2.50e+03 pdb=" O6 DG B 17 " -0.059 2.00e-02 2.50e+03 pdb=" N1 DG B 17 " -0.038 2.00e-02 2.50e+03 pdb=" C2 DG B 17 " 0.005 2.00e-02 2.50e+03 pdb=" N2 DG B 17 " 0.060 2.00e-02 2.50e+03 pdb=" N3 DG B 17 " 0.024 2.00e-02 2.50e+03 pdb=" C4 DG B 17 " -0.002 2.00e-02 2.50e+03 ... (remaining 1167 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 673 2.74 - 3.28: 6809 3.28 - 3.82: 11628 3.82 - 4.36: 12735 4.36 - 4.90: 22795 Nonbonded interactions: 54640 Sorted by model distance: nonbonded pdb=" O GLY A 652 " pdb=" N ALA A 654 " model vdw 2.203 3.120 nonbonded pdb=" O GLU A 489 " pdb=" NH1 ARG A 547 " model vdw 2.253 3.120 nonbonded pdb=" OD2 ASP A 866 " pdb=" NZ LYS A 893 " model vdw 2.333 3.120 nonbonded pdb=" OD2 ASP A 354 " pdb=" NH2 ARG A 659 " model vdw 2.337 3.120 nonbonded pdb=" N ARG A 635 " pdb=" O ARG A 635 " model vdw 2.365 2.496 ... (remaining 54635 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: 2.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 8.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 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 : 0.005 0.049 7365 Z= 0.382 Angle : 0.857 9.977 10177 Z= 0.547 Chirality : 0.087 0.614 1183 Planarity : 0.005 0.073 1170 Dihedral : 19.989 86.963 2668 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.33 % Favored : 93.07 % Rotamer: Outliers : 0.76 % Allowed : 27.69 % Favored : 71.56 % 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: 0.29 (0.31), residues: 837 helix: 1.66 (0.27), residues: 393 sheet: -0.25 (0.48), residues: 140 loop : -1.58 (0.35), residues: 304 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 649 TYR 0.008 0.001 TYR A 842 PHE 0.004 0.001 PHE A 656 TRP 0.006 0.001 TRP A 500 HIS 0.002 0.000 HIS A 797 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.38 ( 7365) covalent geometry : angle 0.85731 / 0.55 (10177) hydrogen bonds : bond 0.17945 / 12.93 ( 330) hydrogen bonds : angle 5.30998 / 4.01 ( 903) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.285 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 53 average time/residue: 0.0774 time to fit residues: 5.7750 Evaluate side-chains 43 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 62 optimal weight: 0.0570 chunk 51 optimal weight: 6.9990 chunk 38 optimal weight: 0.7980 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 203 GLN A 554 ASN A 824 ASN A 939 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.085420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.061063 restraints weight = 17669.685| |-----------------------------------------------------------------------------| r_work (start): 0.2818 rms_B_bonded: 3.07 r_work: 0.2653 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7365 Z= 0.135 Angle : 0.544 7.842 10177 Z= 0.307 Chirality : 0.041 0.144 1183 Planarity : 0.004 0.048 1170 Dihedral : 17.827 86.148 1236 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.57 % Favored : 92.83 % Rotamer: Outliers : 2.87 % Allowed : 25.26 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 837 helix: 2.03 (0.27), residues: 407 sheet: -0.25 (0.47), residues: 139 loop : -1.60 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 277 TYR 0.009 0.001 TYR A 782 PHE 0.005 0.001 PHE A 391 TRP 0.013 0.001 TRP A 445 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.13 ( 7365) covalent geometry : angle 0.54388 / 0.31 (10177) hydrogen bonds : bond 0.05388 / 3.94 ( 330) hydrogen bonds : angle 4.03701 / 2.92 ( 903) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 42 time to evaluate : 0.269 Fit side-chains REVERT: A 858 MET cc_start: 0.7295 (mmm) cc_final: 0.6979 (mmt) REVERT: A 911 CYS cc_start: 0.9287 (m) cc_final: 0.9016 (m) outliers start: 19 outliers final: 9 residues processed: 57 average time/residue: 0.0754 time to fit residues: 6.3446 Evaluate side-chains 53 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 44 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 10 optimal weight: 0.7980 chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 0.8980 chunk 70 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 84 optimal weight: 20.0000 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 68 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 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 = 0.3375 r_free = 0.3375 target = 0.085774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.061533 restraints weight = 17475.766| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.01 r_work: 0.2664 rms_B_bonded: 4.06 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 7365 Z= 0.121 Angle : 0.492 7.530 10177 Z= 0.277 Chirality : 0.039 0.134 1183 Planarity : 0.003 0.045 1170 Dihedral : 17.841 86.609 1236 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.09 % Favored : 93.31 % Rotamer: Outliers : 2.57 % Allowed : 25.42 % Favored : 72.01 % 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: 0.95 (0.31), residues: 837 helix: 2.37 (0.27), residues: 408 sheet: -0.17 (0.47), residues: 139 loop : -1.58 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.007 0.001 TYR A 782 PHE 0.010 0.001 PHE A 656 TRP 0.006 0.001 TRP A 445 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.12 ( 7365) covalent geometry : angle 0.49154 / 0.28 (10177) hydrogen bonds : bond 0.04537 / 3.29 ( 330) hydrogen bonds : angle 3.56712 / 2.57 ( 903) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.323 Fit side-chains REVERT: A 858 MET cc_start: 0.7368 (mmm) cc_final: 0.7004 (mmt) REVERT: A 911 CYS cc_start: 0.9271 (m) cc_final: 0.8986 (m) REVERT: A 988 LEU cc_start: 0.9343 (mt) cc_final: 0.9120 (mt) outliers start: 17 outliers final: 11 residues processed: 60 average time/residue: 0.0715 time to fit residues: 6.6252 Evaluate side-chains 55 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 75 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.085630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.061545 restraints weight = 17682.643| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.95 r_work: 0.2670 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.1399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7365 Z= 0.116 Angle : 0.483 7.223 10177 Z= 0.269 Chirality : 0.039 0.128 1183 Planarity : 0.003 0.038 1170 Dihedral : 17.904 86.176 1236 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.09 % Favored : 93.31 % Rotamer: Outliers : 1.82 % Allowed : 25.87 % Favored : 72.31 % 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: 1.16 (0.31), residues: 837 helix: 2.55 (0.26), residues: 408 sheet: -0.09 (0.47), residues: 139 loop : -1.49 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.008 0.001 TYR A 842 PHE 0.006 0.001 PHE A 656 TRP 0.005 0.001 TRP A 935 HIS 0.004 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.12 ( 7365) covalent geometry : angle 0.48343 / 0.27 (10177) hydrogen bonds : bond 0.04203 / 3.05 ( 330) hydrogen bonds : angle 3.44914 / 2.48 ( 903) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 47 time to evaluate : 0.244 Fit side-chains REVERT: A 221 MET cc_start: 0.9031 (OUTLIER) cc_final: 0.8735 (ttm) REVERT: A 858 MET cc_start: 0.7481 (mmm) cc_final: 0.7088 (mmt) REVERT: A 911 CYS cc_start: 0.9255 (m) cc_final: 0.8967 (m) REVERT: A 988 LEU cc_start: 0.9355 (mt) cc_final: 0.9137 (mt) outliers start: 12 outliers final: 10 residues processed: 55 average time/residue: 0.0577 time to fit residues: 4.9322 Evaluate side-chains 54 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 221 MET Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 0.3980 chunk 16 optimal weight: 0.9980 chunk 69 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3373 r_free = 0.3373 target = 0.084976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.061145 restraints weight = 17546.736| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.02 r_work: 0.2666 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.1509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7365 Z= 0.112 Angle : 0.481 6.939 10177 Z= 0.268 Chirality : 0.039 0.128 1183 Planarity : 0.003 0.039 1170 Dihedral : 17.964 86.630 1236 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.21 % Favored : 93.31 % Rotamer: Outliers : 3.03 % Allowed : 24.81 % Favored : 72.16 % 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: 1.31 (0.31), residues: 837 helix: 2.70 (0.26), residues: 408 sheet: -0.03 (0.47), residues: 139 loop : -1.46 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.007 0.001 TYR A 842 PHE 0.003 0.001 PHE A 656 TRP 0.005 0.001 TRP A 935 HIS 0.005 0.001 HIS A 703 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 7365) covalent geometry : angle 0.48147 / 0.27 (10177) hydrogen bonds : bond 0.04054 / 2.93 ( 330) hydrogen bonds : angle 3.35601 / 2.42 ( 903) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.269 Fit side-chains REVERT: A 701 GLU cc_start: 0.7478 (tm-30) cc_final: 0.7161 (tm-30) REVERT: A 858 MET cc_start: 0.7456 (mmm) cc_final: 0.7053 (mmt) REVERT: A 911 CYS cc_start: 0.9302 (m) cc_final: 0.8987 (m) REVERT: A 988 LEU cc_start: 0.9344 (mt) cc_final: 0.9119 (mt) outliers start: 20 outliers final: 12 residues processed: 61 average time/residue: 0.0635 time to fit residues: 6.0435 Evaluate side-chains 56 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 371 LEU Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 6.9990 chunk 53 optimal weight: 0.0470 chunk 4 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 overall best weight: 0.5478 ------------------------------------------------------------------------------- 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 = 0.3379 r_free = 0.3379 target = 0.085337 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.061524 restraints weight = 17449.240| |-----------------------------------------------------------------------------| r_work (start): 0.2844 rms_B_bonded: 2.93 r_work: 0.2683 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8907 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7365 Z= 0.103 Angle : 0.475 6.924 10177 Z= 0.264 Chirality : 0.039 0.142 1183 Planarity : 0.003 0.043 1170 Dihedral : 17.987 87.154 1236 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.21 % Favored : 93.43 % Rotamer: Outliers : 2.42 % Allowed : 25.42 % Favored : 72.16 % 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: 1.43 (0.32), residues: 837 helix: 2.88 (0.26), residues: 405 sheet: 0.00 (0.47), residues: 139 loop : -1.47 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.007 0.001 TYR A 842 PHE 0.004 0.000 PHE A 938 TRP 0.004 0.001 TRP A 500 HIS 0.004 0.000 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.10 ( 7365) covalent geometry : angle 0.47507 / 0.26 (10177) hydrogen bonds : bond 0.03747 / 2.71 ( 330) hydrogen bonds : angle 3.25408 / 2.34 ( 903) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.267 Fit side-chains REVERT: A 784 TRP cc_start: 0.9251 (t-100) cc_final: 0.9046 (t-100) REVERT: A 858 MET cc_start: 0.7483 (mmm) cc_final: 0.7061 (mmt) REVERT: A 911 CYS cc_start: 0.9215 (m) cc_final: 0.8915 (m) REVERT: A 988 LEU cc_start: 0.9355 (mt) cc_final: 0.9141 (mt) outliers start: 16 outliers final: 12 residues processed: 58 average time/residue: 0.0627 time to fit residues: 5.4070 Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 3.9990 chunk 80 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 75 optimal weight: 0.8980 chunk 72 optimal weight: 0.6980 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3349 r_free = 0.3349 target = 0.084046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.059807 restraints weight = 17600.537| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 3.05 r_work: 0.2645 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8938 moved from start: 0.1716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7365 Z= 0.132 Angle : 0.491 6.682 10177 Z= 0.270 Chirality : 0.039 0.129 1183 Planarity : 0.003 0.039 1170 Dihedral : 18.006 86.598 1236 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.45 % Favored : 93.19 % Rotamer: Outliers : 2.12 % Allowed : 26.02 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.32), residues: 837 helix: 2.94 (0.26), residues: 408 sheet: 0.00 (0.48), residues: 139 loop : -1.45 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.009 0.001 TYR A 842 PHE 0.004 0.001 PHE A 521 TRP 0.007 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 7365) covalent geometry : angle 0.49106 / 0.27 (10177) hydrogen bonds : bond 0.03933 / 2.83 ( 330) hydrogen bonds : angle 3.31330 / 2.39 ( 903) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.236 Fit side-chains REVERT: A 858 MET cc_start: 0.7513 (mmm) cc_final: 0.7079 (mmt) REVERT: A 911 CYS cc_start: 0.9225 (m) cc_final: 0.8910 (m) REVERT: A 988 LEU cc_start: 0.9371 (mt) cc_final: 0.9157 (mt) outliers start: 14 outliers final: 13 residues processed: 54 average time/residue: 0.0648 time to fit residues: 5.3777 Evaluate side-chains 56 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 273 SER Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 26 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 45 optimal weight: 0.1980 chunk 84 optimal weight: 20.0000 chunk 10 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.084581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.060663 restraints weight = 17510.804| |-----------------------------------------------------------------------------| r_work (start): 0.2807 rms_B_bonded: 2.93 r_work: 0.2645 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8930 moved from start: 0.1802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 7365 Z= 0.110 Angle : 0.481 6.852 10177 Z= 0.265 Chirality : 0.039 0.145 1183 Planarity : 0.003 0.040 1170 Dihedral : 18.052 86.975 1236 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.09 % Favored : 93.55 % Rotamer: Outliers : 1.97 % Allowed : 26.17 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.57 (0.32), residues: 837 helix: 2.93 (0.26), residues: 409 sheet: 0.09 (0.47), residues: 139 loop : -1.37 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 977 TYR 0.007 0.001 TYR A 842 PHE 0.004 0.001 PHE A 938 TRP 0.005 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00225 / 0.11 ( 7365) covalent geometry : angle 0.48149 / 0.27 (10177) hydrogen bonds : bond 0.03626 / 2.61 ( 330) hydrogen bonds : angle 3.21413 / 2.31 ( 903) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 46 time to evaluate : 0.206 Fit side-chains REVERT: A 434 LYS cc_start: 0.7649 (pttt) cc_final: 0.7138 (pttm) REVERT: A 858 MET cc_start: 0.7569 (mmm) cc_final: 0.7133 (mmt) REVERT: A 911 CYS cc_start: 0.9129 (m) cc_final: 0.8807 (m) REVERT: A 988 LEU cc_start: 0.9346 (mt) cc_final: 0.9131 (mt) outliers start: 13 outliers final: 13 residues processed: 56 average time/residue: 0.0613 time to fit residues: 5.2729 Evaluate side-chains 55 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.0040 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 74 optimal weight: 0.5980 chunk 12 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- 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 = 0.084343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.060415 restraints weight = 17401.876| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.93 r_work: 0.2647 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8928 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7365 Z= 0.108 Angle : 0.483 8.110 10177 Z= 0.266 Chirality : 0.038 0.127 1183 Planarity : 0.003 0.044 1170 Dihedral : 18.025 87.354 1236 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.21 % Favored : 93.43 % Rotamer: Outliers : 1.97 % Allowed : 25.72 % Favored : 72.31 % 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: 1.62 (0.32), residues: 837 helix: 3.00 (0.27), residues: 408 sheet: 0.10 (0.47), residues: 139 loop : -1.36 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.008 0.001 TYR A 842 PHE 0.004 0.000 PHE A 938 TRP 0.007 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00220 / 0.11 ( 7365) covalent geometry : angle 0.48278 / 0.27 (10177) hydrogen bonds : bond 0.03496 / 2.51 ( 330) hydrogen bonds : angle 3.16877 / 2.28 ( 903) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.279 Fit side-chains REVERT: A 858 MET cc_start: 0.7567 (mmm) cc_final: 0.7124 (mmt) REVERT: A 911 CYS cc_start: 0.9148 (m) cc_final: 0.8832 (m) REVERT: A 988 LEU cc_start: 0.9354 (mt) cc_final: 0.9146 (mt) outliers start: 13 outliers final: 13 residues processed: 53 average time/residue: 0.0674 time to fit residues: 5.5964 Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 841 LEU Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 57 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 36 optimal weight: 0.3980 chunk 69 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 68 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3331 r_free = 0.3331 target = 0.084060 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.060072 restraints weight = 17455.675| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 2.95 r_work: 0.2644 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8933 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 0.033 7365 Z= 0.112 Angle : 0.489 7.269 10177 Z= 0.267 Chirality : 0.039 0.152 1183 Planarity : 0.003 0.039 1170 Dihedral : 17.981 87.368 1236 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.57 % Favored : 93.07 % Rotamer: Outliers : 2.12 % Allowed : 26.02 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.67 (0.32), residues: 837 helix: 3.04 (0.27), residues: 408 sheet: 0.13 (0.47), residues: 139 loop : -1.35 (0.38), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 94 TYR 0.008 0.001 TYR A 842 PHE 0.005 0.000 PHE A 938 TRP 0.009 0.001 TRP A 500 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.11 ( 7365) covalent geometry : angle 0.48926 / 0.27 (10177) hydrogen bonds : bond 0.03466 / 2.48 ( 330) hydrogen bonds : angle 3.15171 / 2.27 ( 903) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1674 Ramachandran restraints generated. 837 Oldfield, 0 Emsley, 837 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 43 time to evaluate : 0.267 Fit side-chains REVERT: A 858 MET cc_start: 0.7554 (mmm) cc_final: 0.7112 (mmt) REVERT: A 911 CYS cc_start: 0.9152 (m) cc_final: 0.8842 (m) REVERT: A 988 LEU cc_start: 0.9355 (mt) cc_final: 0.9145 (mt) outliers start: 14 outliers final: 13 residues processed: 53 average time/residue: 0.0634 time to fit residues: 5.2756 Evaluate side-chains 56 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 286 CYS Chi-restraints excluded: chain A residue 385 MET Chi-restraints excluded: chain A residue 472 VAL Chi-restraints excluded: chain A residue 495 VAL Chi-restraints excluded: chain A residue 501 ASP Chi-restraints excluded: chain A residue 512 SER Chi-restraints excluded: chain A residue 514 VAL Chi-restraints excluded: chain A residue 726 SER Chi-restraints excluded: chain A residue 739 LYS Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 32 optimal weight: 0.1980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.3320 r_free = 0.3320 target = 0.082929 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.059301 restraints weight = 17586.135| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.93 r_work: 0.2621 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8955 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7365 Z= 0.134 Angle : 0.502 9.039 10177 Z= 0.275 Chirality : 0.039 0.131 1183 Planarity : 0.003 0.042 1170 Dihedral : 17.946 86.769 1236 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.21 % Favored : 93.43 % Rotamer: Outliers : 2.12 % Allowed : 26.02 % Favored : 71.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.32), residues: 837 helix: 3.11 (0.27), residues: 407 sheet: 0.13 (0.48), residues: 139 loop : -1.38 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 482 TYR 0.009 0.001 TYR A 842 PHE 0.006 0.001 PHE A 883 TRP 0.007 0.001 TRP A 935 HIS 0.005 0.001 HIS A 806 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 7365) covalent geometry : angle 0.50231 / 0.28 (10177) hydrogen bonds : bond 0.03734 / 2.67 ( 330) hydrogen bonds : angle 3.22452 / 2.33 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1587.26 seconds wall clock time: 27 minutes 54.27 seconds (1674.27 seconds total)