Starting phenix.real_space_refine on Wed Feb 4 18:11:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8vx8_43612/02_2026/8vx8_43612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8vx8_43612/02_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 { model { file = "/net/cci-nas-00/data/ceres_data/8vx8_43612/02_2026/8vx8_43612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8vx8_43612/02_2026/8vx8_43612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8vx8_43612/02_2026/8vx8_43612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8vx8_43612/02_2026/8vx8_43612.map" } 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-2.0-5952/lib/python3.9/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: 2.03, per 1000 atoms: 0.28 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: 0.53 Conformation dependent library (CDL) restraints added in 245.0 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: 0.80 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: 1.51 Time building geometry restraints manager: 0.69 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=" N THR A 636 " pdb=" CA THR A 636 " ideal model delta sigma weight residual 1.457 1.506 -0.049 1.41e-02 5.03e+03 1.20e+01 bond pdb=" C THR A 636 " pdb=" N PRO A 637 " ideal model delta sigma weight residual 1.332 1.368 -0.036 1.32e-02 5.74e+03 7.45e+00 bond pdb=" N LEU A 634 " pdb=" CA LEU A 634 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.26e-02 6.30e+03 6.95e+00 bond pdb=" N ASP A 336 " pdb=" CA ASP A 336 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.23e-02 6.61e+03 6.78e+00 bond pdb=" C ILE A 555 " pdb=" O ILE A 555 " ideal model delta sigma weight residual 1.237 1.209 0.029 1.17e-02 7.31e+03 6.01e+00 ... (remaining 7360 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 9831 2.00 - 3.99: 250 3.99 - 5.99: 58 5.99 - 7.98: 30 7.98 - 9.98: 8 Bond angle restraints: 10177 Sorted by residual: 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 angle pdb=" CA ARG A 635 " pdb=" C ARG A 635 " pdb=" O ARG A 635 " ideal model delta sigma weight residual 121.46 114.52 6.94 1.25e+00 6.40e-01 3.08e+01 angle pdb=" N ILE A 555 " pdb=" CA ILE A 555 " pdb=" C ILE A 555 " ideal model delta sigma weight residual 110.62 106.19 4.43 1.02e+00 9.61e-01 1.89e+01 angle pdb=" O3' DA C 10 " pdb=" P DG C 11 " pdb=" O5' DG C 11 " ideal model delta sigma weight residual 104.00 98.05 5.95 1.50e+00 4.44e-01 1.58e+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 - 0.121: 1141 0.121 - 0.242: 21 0.242 - 0.362: 0 0.362 - 0.483: 2 0.483 - 0.604: 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 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.12e+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 2.35 -2.93 -0.58 2.00e-01 2.50e+01 8.43e+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 2.35 -2.92 -0.58 2.00e-01 2.50e+01 8.38e+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: 1.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.490 Find NCS groups from input model: 0.040 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:1.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 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= 0.249 Angle : 0.837 9.977 10177 Z= 0.446 Chirality : 0.085 0.604 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 covalent geometry : bond 0.00492 ( 7365) covalent geometry : angle 0.83697 (10177) hydrogen bonds : bond 0.17945 ( 330) hydrogen bonds : angle 5.30998 ( 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 : 0.283 Fit side-chains outliers start: 5 outliers final: 0 residues processed: 53 average time/residue: 0.0942 time to fit residues: 6.8172 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 : 0.194 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 203 GLN A 554 ASN A 939 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.085842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.061300 restraints weight = 17696.551| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.07 r_work: 0.2655 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7365 Z= 0.130 Angle : 0.517 7.725 10177 Z= 0.283 Chirality : 0.039 0.141 1183 Planarity : 0.003 0.036 1170 Dihedral : 17.673 85.621 1236 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.33 % Favored : 93.07 % Rotamer: Outliers : 1.82 % Allowed : 26.17 % 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: 0.76 (0.31), residues: 837 helix: 2.15 (0.27), residues: 407 sheet: -0.21 (0.48), residues: 139 loop : -1.58 (0.36), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 547 TYR 0.009 0.001 TYR A 212 PHE 0.004 0.001 PHE A 391 TRP 0.014 0.001 TRP A 445 HIS 0.003 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7365) covalent geometry : angle 0.51669 (10177) hydrogen bonds : bond 0.04704 ( 330) hydrogen bonds : angle 3.78623 ( 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 54 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.292 Fit side-chains REVERT: A 858 MET cc_start: 0.7295 (mmm) cc_final: 0.6955 (mmt) REVERT: A 911 CYS cc_start: 0.9271 (m) cc_final: 0.9011 (m) REVERT: A 988 LEU cc_start: 0.9339 (mt) cc_final: 0.9110 (mt) outliers start: 12 outliers final: 6 residues processed: 51 average time/residue: 0.0696 time to fit residues: 5.4294 Evaluate side-chains 49 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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: 1.9990 chunk 85 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 70 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 84 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 68 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.084493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060551 restraints weight = 17441.812| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.00 r_work: 0.2639 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8786 moved from start: 0.1334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7365 Z= 0.133 Angle : 0.488 7.017 10177 Z= 0.267 Chirality : 0.039 0.137 1183 Planarity : 0.003 0.038 1170 Dihedral : 17.541 84.537 1236 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.60 % Allowed : 5.85 % Favored : 93.55 % Rotamer: Outliers : 2.57 % Allowed : 25.11 % 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: 1.06 (0.31), residues: 837 helix: 2.48 (0.27), residues: 408 sheet: -0.11 (0.48), residues: 139 loop : -1.57 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 547 TYR 0.009 0.001 TYR A 842 PHE 0.004 0.001 PHE A 883 TRP 0.009 0.001 TRP A 935 HIS 0.003 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7365) covalent geometry : angle 0.48795 (10177) hydrogen bonds : bond 0.04269 ( 330) hydrogen bonds : angle 3.48686 ( 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 : 0.247 Fit side-chains REVERT: A 858 MET cc_start: 0.7480 (mmm) cc_final: 0.7064 (mmt) REVERT: A 911 CYS cc_start: 0.9269 (m) cc_final: 0.9042 (m) REVERT: A 988 LEU cc_start: 0.9352 (mt) cc_final: 0.9138 (mt) outliers start: 17 outliers final: 11 residues processed: 61 average time/residue: 0.0754 time to fit residues: 6.6594 Evaluate side-chains 56 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 45 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL 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 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 65 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 824 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.083814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060085 restraints weight = 17814.092| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 3.06 r_work: 0.2647 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 7365 Z= 0.125 Angle : 0.482 6.927 10177 Z= 0.261 Chirality : 0.039 0.134 1183 Planarity : 0.003 0.043 1170 Dihedral : 17.575 84.165 1236 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.60 % Allowed : 6.45 % Favored : 92.95 % Rotamer: Outliers : 2.27 % Allowed : 25.57 % 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: 1.27 (0.32), residues: 837 helix: 2.69 (0.27), residues: 407 sheet: -0.07 (0.47), residues: 139 loop : -1.50 (0.37), residues: 291 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 0.003 0.000 PHE A 521 TRP 0.009 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 7365) covalent geometry : angle 0.48213 (10177) hydrogen bonds : bond 0.03845 ( 330) hydrogen bonds : angle 3.37103 ( 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 63 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 48 time to evaluate : 0.225 Fit side-chains REVERT: A 858 MET cc_start: 0.7500 (mmm) cc_final: 0.7041 (mmt) REVERT: A 911 CYS cc_start: 0.9208 (m) cc_final: 0.8995 (m) REVERT: A 988 LEU cc_start: 0.9351 (mt) cc_final: 0.9140 (mt) outliers start: 15 outliers final: 11 residues processed: 59 average time/residue: 0.0652 time to fit residues: 5.8983 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 : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 69 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 26 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 64 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.058656 restraints weight = 17705.004| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 3.01 r_work: 0.2617 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8851 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 7365 Z= 0.154 Angle : 0.499 6.622 10177 Z= 0.270 Chirality : 0.040 0.139 1183 Planarity : 0.003 0.047 1170 Dihedral : 17.635 83.278 1236 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.48 % Allowed : 5.97 % Favored : 93.55 % Rotamer: Outliers : 2.72 % Allowed : 24.96 % 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: 1.33 (0.32), residues: 837 helix: 2.78 (0.27), residues: 407 sheet: -0.07 (0.48), residues: 139 loop : -1.50 (0.38), residues: 291 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 547 TYR 0.011 0.001 TYR A 842 PHE 0.004 0.001 PHE A 883 TRP 0.008 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 7365) covalent geometry : angle 0.49905 (10177) hydrogen bonds : bond 0.04207 ( 330) hydrogen bonds : angle 3.42203 ( 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 58 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 40 time to evaluate : 0.207 Fit side-chains REVERT: A 858 MET cc_start: 0.7582 (mmm) cc_final: 0.7141 (mmt) REVERT: A 988 LEU cc_start: 0.9349 (mt) cc_final: 0.9142 (mt) outliers start: 18 outliers final: 11 residues processed: 54 average time/residue: 0.0651 time to fit residues: 5.3411 Evaluate side-chains 48 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 37 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 THR 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 726 SER 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: 0.9980 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.7980 chunk 63 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.059324 restraints weight = 17555.696| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 2.96 r_work: 0.2629 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7365 Z= 0.117 Angle : 0.492 7.405 10177 Z= 0.265 Chirality : 0.039 0.140 1183 Planarity : 0.003 0.048 1170 Dihedral : 17.668 84.162 1236 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.09 % Favored : 93.43 % Rotamer: Outliers : 3.03 % Allowed : 24.96 % 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: 1.41 (0.32), residues: 837 helix: 2.83 (0.26), residues: 407 sheet: -0.01 (0.47), residues: 139 loop : -1.45 (0.38), residues: 291 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 0.003 0.001 PHE A 938 TRP 0.006 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 7365) covalent geometry : angle 0.49153 (10177) hydrogen bonds : bond 0.03639 ( 330) hydrogen bonds : angle 3.25817 ( 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 62 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 42 time to evaluate : 0.277 Fit side-chains REVERT: A 547 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8671 (tpp-160) REVERT: A 858 MET cc_start: 0.7605 (mmm) cc_final: 0.7091 (mmt) outliers start: 20 outliers final: 14 residues processed: 58 average time/residue: 0.0641 time to fit residues: 5.5678 Evaluate side-chains 57 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.188 ------------------------------------------------------------------------------- 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 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 547 ARG 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 Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 30 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 75 optimal weight: 0.4980 chunk 72 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.083015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.059440 restraints weight = 17601.265| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.97 r_work: 0.2638 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7365 Z= 0.114 Angle : 0.484 7.546 10177 Z= 0.258 Chirality : 0.039 0.141 1183 Planarity : 0.003 0.043 1170 Dihedral : 17.618 84.205 1236 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.48 % Allowed : 6.45 % Favored : 93.07 % Rotamer: Outliers : 2.87 % Allowed : 26.02 % Favored : 71.10 % 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: 1.50 (0.32), residues: 837 helix: 2.91 (0.26), residues: 407 sheet: 0.01 (0.47), residues: 139 loop : -1.40 (0.38), residues: 291 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 0.003 0.000 PHE A 380 TRP 0.006 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 7365) covalent geometry : angle 0.48373 (10177) hydrogen bonds : bond 0.03439 ( 330) hydrogen bonds : angle 3.16931 ( 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 62 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 43 time to evaluate : 0.205 Fit side-chains REVERT: A 547 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8697 (tpp-160) REVERT: A 858 MET cc_start: 0.7619 (mmm) cc_final: 0.7110 (mmt) outliers start: 19 outliers final: 13 residues processed: 59 average time/residue: 0.0683 time to fit residues: 5.8862 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 : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 234 THR Chi-restraints excluded: chain A residue 273 SER 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 547 ARG Chi-restraints excluded: chain A residue 850 LEU Chi-restraints excluded: chain A residue 908 SER Chi-restraints excluded: chain A residue 981 VAL Chi-restraints excluded: chain A residue 985 ILE 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: 3.9990 chunk 45 optimal weight: 0.7980 chunk 84 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 62 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 21 optimal weight: 0.8980 chunk 56 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.082735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.059427 restraints weight = 17674.564| |-----------------------------------------------------------------------------| r_work (start): 0.2785 rms_B_bonded: 2.96 r_work: 0.2624 rms_B_bonded: 3.92 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8829 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7365 Z= 0.120 Angle : 0.499 7.765 10177 Z= 0.268 Chirality : 0.039 0.142 1183 Planarity : 0.003 0.047 1170 Dihedral : 17.575 84.405 1236 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.45 % Favored : 93.19 % Rotamer: Outliers : 2.27 % Allowed : 26.48 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.56 (0.32), residues: 837 helix: 2.96 (0.26), residues: 407 sheet: 0.06 (0.47), residues: 139 loop : -1.40 (0.38), residues: 291 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 0.003 0.000 PHE A 938 TRP 0.006 0.001 TRP A 935 HIS 0.004 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00272 ( 7365) covalent geometry : angle 0.49914 (10177) hydrogen bonds : bond 0.03451 ( 330) hydrogen bonds : angle 3.19937 ( 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 58 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.264 Fit side-chains REVERT: A 547 ARG cc_start: 0.8940 (OUTLIER) cc_final: 0.8709 (tpp-160) REVERT: A 858 MET cc_start: 0.7613 (mmm) cc_final: 0.7092 (mmt) outliers start: 15 outliers final: 14 residues processed: 54 average time/residue: 0.0715 time to fit residues: 5.6053 Evaluate side-chains 58 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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 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 547 ARG 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 Chi-restraints excluded: chain A residue 985 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 50 optimal weight: 0.0980 chunk 79 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 12 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.083133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.059879 restraints weight = 17541.565| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 2.97 r_work: 0.2635 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8820 moved from start: 0.2170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 7365 Z= 0.110 Angle : 0.494 7.926 10177 Z= 0.263 Chirality : 0.038 0.131 1183 Planarity : 0.003 0.044 1170 Dihedral : 17.533 84.647 1236 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.33 % Favored : 93.31 % Rotamer: Outliers : 2.27 % Allowed : 26.32 % Favored : 71.41 % 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: 1.60 (0.32), residues: 837 helix: 2.97 (0.26), residues: 408 sheet: 0.11 (0.47), residues: 139 loop : -1.37 (0.38), residues: 290 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 0.003 0.000 PHE A 516 TRP 0.007 0.001 TRP A 935 HIS 0.003 0.001 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00248 ( 7365) covalent geometry : angle 0.49361 (10177) hydrogen bonds : bond 0.03230 ( 330) hydrogen bonds : angle 3.12228 ( 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 60 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 45 time to evaluate : 0.262 Fit side-chains REVERT: A 547 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8712 (tpp-160) REVERT: A 858 MET cc_start: 0.7634 (mmm) cc_final: 0.7119 (mmt) outliers start: 15 outliers final: 13 residues processed: 56 average time/residue: 0.0642 time to fit residues: 5.3593 Evaluate side-chains 59 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 45 time to evaluate : 0.168 ------------------------------------------------------------------------------- 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 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 547 ARG 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: 0.4980 chunk 14 optimal weight: 7.9990 chunk 43 optimal weight: 0.5980 chunk 83 optimal weight: 0.0270 chunk 39 optimal weight: 0.0170 chunk 36 optimal weight: 0.1980 chunk 69 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 79 optimal weight: 0.7980 overall best weight: 0.2676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.084760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.061465 restraints weight = 17416.521| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.95 r_work: 0.2680 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 7365 Z= 0.098 Angle : 0.498 9.135 10177 Z= 0.266 Chirality : 0.038 0.152 1183 Planarity : 0.003 0.045 1170 Dihedral : 17.478 86.019 1236 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.09 % Favored : 93.55 % Rotamer: Outliers : 1.66 % Allowed : 27.23 % Favored : 71.10 % 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: 1.66 (0.32), residues: 837 helix: 2.97 (0.26), residues: 409 sheet: 0.21 (0.47), residues: 139 loop : -1.31 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 547 TYR 0.006 0.001 TYR A 782 PHE 0.004 0.000 PHE A 516 TRP 0.005 0.001 TRP A 592 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00212 ( 7365) covalent geometry : angle 0.49825 (10177) hydrogen bonds : bond 0.02844 ( 330) hydrogen bonds : angle 3.01013 ( 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 55 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.221 Fit side-chains REVERT: A 434 LYS cc_start: 0.7379 (pttt) cc_final: 0.7011 (pttm) REVERT: A 858 MET cc_start: 0.7641 (mmm) cc_final: 0.7336 (mmm) outliers start: 11 outliers final: 9 residues processed: 52 average time/residue: 0.0691 time to fit residues: 5.2856 Evaluate side-chains 50 residues out of total 755 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.278 ------------------------------------------------------------------------------- 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 385 MET Chi-restraints excluded: chain A residue 472 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 4.9990 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.3980 chunk 32 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 31 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 75 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.083919 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.060647 restraints weight = 17582.855| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 2.94 r_work: 0.2655 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8801 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 7365 Z= 0.108 Angle : 0.509 8.373 10177 Z= 0.269 Chirality : 0.038 0.171 1183 Planarity : 0.003 0.043 1170 Dihedral : 17.437 85.726 1236 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.36 % Allowed : 6.45 % Favored : 93.19 % Rotamer: Outliers : 1.51 % Allowed : 27.69 % Favored : 70.80 % 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: 1.74 (0.32), residues: 837 helix: 3.03 (0.27), residues: 409 sheet: 0.30 (0.48), residues: 139 loop : -1.30 (0.38), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 547 TYR 0.006 0.001 TYR A 842 PHE 0.003 0.000 PHE A 516 TRP 0.008 0.001 TRP A 500 HIS 0.003 0.000 HIS A 806 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 7365) covalent geometry : angle 0.50857 (10177) hydrogen bonds : bond 0.02997 ( 330) hydrogen bonds : angle 3.00283 ( 903) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1471.07 seconds wall clock time: 25 minutes 47.45 seconds (1547.45 seconds total)