Starting phenix.real_space_refine on Wed Aug 5 21:46:00 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9qia_53183/08_2026/9qia_53183.map" } resolution = 4.38 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 7 5.49 5 S 52 5.16 5 C 7260 2.51 5 N 1934 2.21 5 O 2175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 64 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11428 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 291, 2331 Classifications: {'peptide': 291} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 273} Chain: "B" Number of atoms: 7834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 988, 7834 Classifications: {'peptide': 988} Link IDs: {'CIS': 1, 'PCIS': 4, 'PTRANS': 47, 'TRANS': 935} Chain breaks: 1 Chain: "C" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'IHP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 22 Unusual residues: {'AMP%rna2p': 1} Classifications: {'RNA_mixed': 1} Modifications used: {'rna2p': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 1.90, per 1000 atoms: 0.17 Number of scatterers: 11428 At special positions: 0 Unit cell: (94.35, 100.3, 131.75, 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 52 16.00 P 7 15.00 O 2175 8.00 N 1934 7.00 C 7260 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 430.1 milliseconds 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2716 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 47.7% alpha, 12.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 4524 through 4533 Processing helix chain 'A' and resid 4559 through 4566 Processing helix chain 'A' and resid 4572 through 4586 removed outlier: 3.777A pdb=" N VAL A4583 " --> pdb=" O ALA A4579 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N THR A4584 " --> pdb=" O GLN A4580 " (cutoff:3.500A) Processing helix chain 'A' and resid 4667 through 4671 Processing helix chain 'A' and resid 4687 through 4699 Processing helix chain 'A' and resid 4703 through 4708 removed outlier: 3.833A pdb=" N PHE A4706 " --> pdb=" O GLU A4703 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A4708 " --> pdb=" O TYR A4705 " (cutoff:3.500A) Processing helix chain 'A' and resid 4711 through 4715 Processing helix chain 'A' and resid 4717 through 4739 Processing helix chain 'A' and resid 4740 through 4746 Processing helix chain 'A' and resid 4751 through 4762 Processing helix chain 'A' and resid 4762 through 4780 removed outlier: 4.162A pdb=" N TYR A4780 " --> pdb=" O ASP A4776 " (cutoff:3.500A) Processing helix chain 'A' and resid 4786 through 4810 removed outlier: 3.689A pdb=" N GLN A4803 " --> pdb=" O ARG A4799 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N GLU A4806 " --> pdb=" O ALA A4802 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 52 removed outlier: 7.288A pdb=" N ARG B 46 " --> pdb=" O ALA B 42 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLN B 47 " --> pdb=" O LEU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 70 through 84 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 108 through 115 Processing helix chain 'B' and resid 117 through 128 removed outlier: 3.949A pdb=" N VAL B 122 " --> pdb=" O ARG B 118 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 123 " --> pdb=" O ALA B 119 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LYS B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N HIS B 125 " --> pdb=" O ALA B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 154 removed outlier: 3.514A pdb=" N ASP B 152 " --> pdb=" O SER B 149 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS B 153 " --> pdb=" O PHE B 150 " (cutoff:3.500A) Processing helix chain 'B' and resid 163 through 176 Processing helix chain 'B' and resid 253 through 257 Processing helix chain 'B' and resid 301 through 308 removed outlier: 3.756A pdb=" N LYS B 307 " --> pdb=" O GLU B 303 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N HIS B 308 " --> pdb=" O ARG B 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 340 removed outlier: 3.583A pdb=" N GLU B 324 " --> pdb=" O GLU B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 365 removed outlier: 3.639A pdb=" N GLU B 363 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 364 " --> pdb=" O SER B 360 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 382 Processing helix chain 'B' and resid 387 through 408 Processing helix chain 'B' and resid 421 through 427 removed outlier: 4.466A pdb=" N VAL B 425 " --> pdb=" O ALA B 421 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N SER B 427 " --> pdb=" O ASP B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 432 through 437 Processing helix chain 'B' and resid 443 through 450 Processing helix chain 'B' and resid 451 through 459 removed outlier: 3.626A pdb=" N CYS B 455 " --> pdb=" O GLY B 451 " (cutoff:3.500A) Processing helix chain 'B' and resid 469 through 483 removed outlier: 3.535A pdb=" N CYS B 473 " --> pdb=" O GLY B 469 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N GLU B 474 " --> pdb=" O ALA B 470 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 509 removed outlier: 4.314A pdb=" N ARG B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 513 through 517 removed outlier: 3.876A pdb=" N ILE B 517 " --> pdb=" O PRO B 514 " (cutoff:3.500A) Processing helix chain 'B' and resid 520 through 531 removed outlier: 3.877A pdb=" N LYS B 531 " --> pdb=" O ASP B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 552 removed outlier: 4.201A pdb=" N THR B 551 " --> pdb=" O THR B 548 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 561 Processing helix chain 'B' and resid 570 through 583 Processing helix chain 'B' and resid 610 through 614 removed outlier: 3.561A pdb=" N HIS B 614 " --> pdb=" O TYR B 611 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 628 Processing helix chain 'B' and resid 633 through 650 removed outlier: 3.563A pdb=" N THR B 637 " --> pdb=" O ALA B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 663 Processing helix chain 'B' and resid 665 through 675 Processing helix chain 'B' and resid 681 through 691 Processing helix chain 'B' and resid 695 through 712 Processing helix chain 'B' and resid 712 through 722 removed outlier: 3.516A pdb=" N LEU B 716 " --> pdb=" O ASN B 712 " (cutoff:3.500A) Processing helix chain 'B' and resid 751 through 769 Processing helix chain 'B' and resid 774 through 778 Processing helix chain 'B' and resid 779 through 788 Processing helix chain 'B' and resid 821 through 834 Processing helix chain 'B' and resid 839 through 843 removed outlier: 3.567A pdb=" N GLN B 843 " --> pdb=" O SER B 840 " (cutoff:3.500A) Processing helix chain 'B' and resid 857 through 873 removed outlier: 3.848A pdb=" N TYR B 873 " --> pdb=" O ARG B 869 " (cutoff:3.500A) Processing helix chain 'B' and resid 879 through 889 Processing helix chain 'B' and resid 894 through 915 removed outlier: 3.548A pdb=" N THR B 898 " --> pdb=" O ILE B 894 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ILE B 910 " --> pdb=" O ALA B 906 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS B 911 " --> pdb=" O LEU B 907 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLY B 915 " --> pdb=" O LYS B 911 " (cutoff:3.500A) Processing helix chain 'B' and resid 967 through 980 Processing helix chain 'B' and resid 1001 through 1007 removed outlier: 3.676A pdb=" N LYS B1006 " --> pdb=" O LYS B1003 " (cutoff:3.500A) Processing helix chain 'B' and resid 1008 through 1014 Processing helix chain 'C' and resid 22 through 34 Processing helix chain 'C' and resid 56 through 60 removed outlier: 3.594A pdb=" N TYR C 59 " --> pdb=" O LEU C 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 35 removed outlier: 3.577A pdb=" N ILE E 30 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN E 31 " --> pdb=" O LYS E 27 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASP E 32 " --> pdb=" O ALA E 28 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N LYS E 33 " --> pdb=" O LYS E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 41 removed outlier: 3.553A pdb=" N GLN E 41 " --> pdb=" O PRO E 38 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 60 removed outlier: 3.735A pdb=" N TYR E 59 " --> pdb=" O THR E 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4537 through 4540 removed outlier: 3.839A pdb=" N CYS A4601 " --> pdb=" O ASP A4538 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N ILE A4608 " --> pdb=" O ASP A4602 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE A4626 " --> pdb=" O ILE A4613 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 4543 through 4545 Processing sheet with id=AA3, first strand: chain 'B' and resid 134 through 138 removed outlier: 6.134A pdb=" N VAL B 64 " --> pdb=" O THR B 89 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N HIS B 91 " --> pdb=" O VAL B 64 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N LEU B 66 " --> pdb=" O HIS B 91 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N HIS B 63 " --> pdb=" O CYS B 156 " (cutoff:3.500A) removed outlier: 8.494A pdb=" N VAL B 158 " --> pdb=" O HIS B 63 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N PHE B 65 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER B 185 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 203 through 205 Processing sheet with id=AA5, first strand: chain 'B' and resid 218 through 222 removed outlier: 3.709A pdb=" N ILE B 228 " --> pdb=" O THR B 222 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N SER B 272 " --> pdb=" O VAL B 265 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N VAL B 265 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 260 through 262 removed outlier: 4.581A pdb=" N PHE B 244 " --> pdb=" O VAL B 291 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 538 through 541 removed outlier: 6.545A pdb=" N ILE B 493 " --> pdb=" O ASP B 539 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N HIS B 541 " --> pdb=" O ILE B 493 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL B 495 " --> pdb=" O HIS B 541 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 496 " --> pdb=" O LEU B 465 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N ASN B 462 " --> pdb=" O VAL B 563 " (cutoff:3.500A) removed outlier: 8.197A pdb=" N ILE B 565 " --> pdb=" O ASN B 462 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N PHE B 464 " --> pdb=" O ILE B 565 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N ILE B 564 " --> pdb=" O LEU B 589 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N SER B 591 " --> pdb=" O ILE B 564 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR B 566 " --> pdb=" O SER B 591 " (cutoff:3.500A) removed outlier: 9.301A pdb=" N THR B 593 " --> pdb=" O THR B 566 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LEU B 588 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N CYS B 924 " --> pdb=" O THR B 600 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 944 through 945 Processing sheet with id=AA9, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.670A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B1043 " --> pdb=" O LEU B1024 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER B1027 " --> pdb=" O MET B 985 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N MET B 985 " --> pdb=" O SER B1027 " (cutoff:3.500A) removed outlier: 5.050A pdb=" N GLN B 988 " --> pdb=" O MET B 992 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N MET B 992 " --> pdb=" O GLN B 988 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 958 through 961 removed outlier: 6.670A pdb=" N TRP B 958 " --> pdb=" O ARG B1044 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N TYR B1046 " --> pdb=" O TRP B 958 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VAL B 960 " --> pdb=" O TYR B1046 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL B1043 " --> pdb=" O LEU B1024 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 48 through 49 removed outlier: 3.885A pdb=" N HIS C 68 " --> pdb=" O ILE C 44 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 12 through 16 removed outlier: 4.259A pdb=" N SER E 65 " --> pdb=" O GLN E 2 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG E 42 " --> pdb=" O VAL E 70 " (cutoff:3.500A) 513 hydrogen bonds defined for protein. 1413 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.78 Time building geometry restraints manager: 0.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3728 1.35 - 1.47: 2606 1.47 - 1.59: 5259 1.59 - 1.71: 7 1.71 - 1.83: 77 Bond restraints: 11677 Sorted by residual: bond pdb=" N ILE B 622 " pdb=" CA ILE B 622 " ideal model delta sigma weight residual 1.456 1.493 -0.036 8.70e-03 1.32e+04 1.72e+01 bond pdb=" CA SER E 20 " pdb=" CB SER E 20 " ideal model delta sigma weight residual 1.539 1.498 0.040 1.20e-02 6.94e+03 1.13e+01 bond pdb=" N ASN A4656 " pdb=" CA ASN A4656 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.18e-02 7.18e+03 8.40e+00 bond pdb=" CZ ARG A4654 " pdb=" NH2 ARG A4654 " ideal model delta sigma weight residual 1.330 1.297 0.033 1.30e-02 5.92e+03 6.57e+00 bond pdb=" CZ ARG C 74 " pdb=" NH2 ARG C 74 " ideal model delta sigma weight residual 1.330 1.298 0.032 1.30e-02 5.92e+03 5.98e+00 ... (remaining 11672 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 15261 1.34 - 2.68: 421 2.68 - 4.02: 117 4.02 - 5.36: 23 5.36 - 6.70: 8 Bond angle restraints: 15830 Sorted by residual: angle pdb=" N CYS A4666 " pdb=" CA CYS A4666 " pdb=" CB CYS A4666 " ideal model delta sigma weight residual 110.65 103.95 6.70 1.56e+00 4.11e-01 1.85e+01 angle pdb=" CA ARG C 74 " pdb=" C ARG C 74 " pdb=" N GLY C 75 " ideal model delta sigma weight residual 115.51 120.83 -5.32 1.24e+00 6.50e-01 1.84e+01 angle pdb=" CA THR E 22 " pdb=" CB THR E 22 " pdb=" OG1 THR E 22 " ideal model delta sigma weight residual 109.60 103.44 6.16 1.50e+00 4.44e-01 1.69e+01 angle pdb=" CA PRO E 19 " pdb=" C PRO E 19 " pdb=" O PRO E 19 " ideal model delta sigma weight residual 121.95 117.33 4.62 1.25e+00 6.40e-01 1.37e+01 angle pdb=" N SER B 625 " pdb=" CA SER B 625 " pdb=" C SER B 625 " ideal model delta sigma weight residual 111.33 106.97 4.36 1.21e+00 6.83e-01 1.30e+01 ... (remaining 15825 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.80: 6584 16.80 - 33.61: 413 33.61 - 50.41: 98 50.41 - 67.22: 17 67.22 - 84.02: 4 Dihedral angle restraints: 7116 sinusoidal: 2935 harmonic: 4181 Sorted by residual: dihedral pdb=" CA SER B 625 " pdb=" C SER B 625 " pdb=" N THR B 626 " pdb=" CA THR B 626 " ideal model delta harmonic sigma weight residual 180.00 156.27 23.73 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ASP C 52 " pdb=" C ASP C 52 " pdb=" N GLY C 53 " pdb=" CA GLY C 53 " ideal model delta harmonic sigma weight residual 180.00 -158.56 -21.44 0 5.00e+00 4.00e-02 1.84e+01 dihedral pdb=" CA LYS C 63 " pdb=" C LYS C 63 " pdb=" N GLU C 64 " pdb=" CA GLU C 64 " ideal model delta harmonic sigma weight residual 180.00 159.61 20.39 0 5.00e+00 4.00e-02 1.66e+01 ... (remaining 7113 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 1570 0.064 - 0.128: 200 0.128 - 0.193: 10 0.193 - 0.257: 2 0.257 - 0.321: 1 Chirality restraints: 1783 Sorted by residual: chirality pdb=" CA ARG C 74 " pdb=" N ARG C 74 " pdb=" C ARG C 74 " pdb=" CB ARG C 74 " both_signs ideal model delta sigma weight residual False 2.51 2.83 -0.32 2.00e-01 2.50e+01 2.58e+00 chirality pdb=" CA PHE B 624 " pdb=" N PHE B 624 " pdb=" C PHE B 624 " pdb=" CB PHE B 624 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE B 622 " pdb=" N ILE B 622 " pdb=" C ILE B 622 " pdb=" CB ILE B 622 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1780 not shown) Planarity restraints: 2030 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A4673 " 0.072 2.00e-02 2.50e+03 3.37e-02 2.83e+01 pdb=" CG TRP A4673 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A4673 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A4673 " -0.040 2.00e-02 2.50e+03 pdb=" NE1 TRP A4673 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP A4673 " -0.005 2.00e-02 2.50e+03 pdb=" CE3 TRP A4673 " -0.038 2.00e-02 2.50e+03 pdb=" CZ2 TRP A4673 " 0.026 2.00e-02 2.50e+03 pdb=" CZ3 TRP A4673 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A4673 " 0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 625 " 0.020 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C SER B 625 " -0.069 2.00e-02 2.50e+03 pdb=" O SER B 625 " 0.026 2.00e-02 2.50e+03 pdb=" N THR B 626 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A4654 " 0.152 9.50e-02 1.11e+02 6.81e-02 2.95e+00 pdb=" NE ARG A4654 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG A4654 " -0.007 2.00e-02 2.50e+03 pdb=" NH1 ARG A4654 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG A4654 " 0.007 2.00e-02 2.50e+03 ... (remaining 2027 not shown) Histogram of nonbonded interaction distances: 1.32 - 2.04: 2 2.04 - 2.75: 1357 2.75 - 3.47: 17502 3.47 - 4.18: 27332 4.18 - 4.90: 47627 Nonbonded interactions: 93820 Sorted by model distance: nonbonded pdb=" OG SER B 625 " pdb=" C ALA C 76 " model vdw 1.324 3.270 nonbonded pdb=" SG CYS A4666 " pdb=" CB ALA C 76 " model vdw 1.835 3.820 nonbonded pdb=" OG SER B 625 " pdb=" O ALA C 76 " model vdw 2.223 3.040 nonbonded pdb=" CB ASN A4671 " pdb=" CZ3 TRP A4673 " model vdw 2.315 3.740 nonbonded pdb=" CD1 TYR B 611 " pdb=" NH1 ARG E 72 " model vdw 2.372 3.420 ... (remaining 93815 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 Found NCS groups: ncs_group { reference = chain 'C' selection = (chain 'E' and (resid 1 through 75 or (resid 76 and (name N or name CA or name C \ or name O or name CB )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.200 Find NCS groups from input model: 0.070 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: 0.020 Load rotamer database and sin/cos tables:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11678 Z= 0.176 Angle : 0.592 6.703 15830 Z= 0.336 Chirality : 0.043 0.321 1783 Planarity : 0.004 0.068 2030 Dihedral : 12.011 84.021 4400 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.47 % Allowed : 1.18 % Favored : 98.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.05 (0.23), residues: 1421 helix: 1.57 (0.22), residues: 566 sheet: 0.42 (0.35), residues: 208 loop : 0.10 (0.26), residues: 647 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A4654 TYR 0.011 0.001 TYR A4660 PHE 0.013 0.001 PHE B 966 TRP 0.072 0.003 TRP A4673 HIS 0.005 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.18 (11677) covalent geometry : angle 0.59220 / 0.34 (15830) hydrogen bonds : bond 0.16808 / 10.87 ( 510) hydrogen bonds : angle 6.68401 / 4.63 ( 1413) Misc. bond : bond 0.00123 / 0.06 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.9062 (mtp) cc_final: 0.8835 (mtp) REVERT: A 4626 PHE cc_start: 0.9123 (m-80) cc_final: 0.8915 (m-80) REVERT: B 69 MET cc_start: 0.8611 (mmp) cc_final: 0.7888 (mmm) REVERT: B 329 MET cc_start: 0.9770 (mmm) cc_final: 0.9270 (mmm) REVERT: B 479 PHE cc_start: 0.9761 (m-80) cc_final: 0.9376 (m-80) REVERT: B 492 MET cc_start: 0.8918 (tpt) cc_final: 0.8707 (tpt) REVERT: B 844 MET cc_start: 0.8953 (pmm) cc_final: 0.8306 (pmm) REVERT: C 3 ILE cc_start: 0.8887 (tp) cc_final: 0.8583 (mp) REVERT: E 1 MET cc_start: 0.7756 (OUTLIER) cc_final: 0.6804 (tmm) REVERT: E 14 THR cc_start: 0.9228 (m) cc_final: 0.8811 (t) REVERT: E 33 LYS cc_start: 0.7966 (mtpt) cc_final: 0.7481 (tptt) outliers start: 6 outliers final: 2 residues processed: 86 average time/residue: 0.0749 time to fit residues: 9.8734 Evaluate side-chains 63 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 98 optimal weight: 6.9990 chunk 107 optimal weight: 0.7980 chunk 10 optimal weight: 9.9990 chunk 66 optimal weight: 9.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4536 GLN A4696 GLN B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3044 r_free = 0.3044 target = 0.038654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.032888 restraints weight = 168636.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033691 restraints weight = 105166.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034252 restraints weight = 73689.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.034677 restraints weight = 55321.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.034996 restraints weight = 43741.664| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 11678 Z= 0.147 Angle : 0.534 6.757 15830 Z= 0.282 Chirality : 0.040 0.166 1783 Planarity : 0.004 0.043 2030 Dihedral : 5.215 48.449 1576 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.26 (0.23), residues: 1421 helix: 1.76 (0.22), residues: 577 sheet: 0.70 (0.34), residues: 195 loop : 0.13 (0.26), residues: 649 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 74 TYR 0.019 0.001 TYR A4528 PHE 0.015 0.001 PHE A4598 TRP 0.010 0.001 TRP A4673 HIS 0.007 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.15 (11677) covalent geometry : angle 0.53433 / 0.28 (15830) hydrogen bonds : bond 0.03763 / 2.47 ( 510) hydrogen bonds : angle 5.10539 / 3.57 ( 1413) Misc. bond : bond 0.00022 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8754 (mtp) cc_final: 0.8404 (mtp) REVERT: B 69 MET cc_start: 0.8554 (mmp) cc_final: 0.7846 (mmm) REVERT: B 329 MET cc_start: 0.9735 (mmm) cc_final: 0.9228 (mmm) REVERT: B 479 PHE cc_start: 0.9767 (m-80) cc_final: 0.9405 (m-80) REVERT: B 591 SER cc_start: 0.9126 (m) cc_final: 0.8912 (t) REVERT: B 844 MET cc_start: 0.8768 (pmm) cc_final: 0.8215 (pmm) REVERT: C 3 ILE cc_start: 0.8829 (tp) cc_final: 0.8490 (mp) REVERT: E 1 MET cc_start: 0.8039 (ttp) cc_final: 0.6733 (tmm) REVERT: E 14 THR cc_start: 0.9039 (m) cc_final: 0.8803 (t) REVERT: E 33 LYS cc_start: 0.7909 (mtpt) cc_final: 0.7534 (tptt) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.0807 time to fit residues: 8.8914 Evaluate side-chains 59 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 87 optimal weight: 0.0570 chunk 71 optimal weight: 8.9990 chunk 75 optimal weight: 4.9990 chunk 110 optimal weight: 6.9990 chunk 127 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 109 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 10.0000 overall best weight: 2.4106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4696 GLN B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.038963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.033095 restraints weight = 168706.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.033900 restraints weight = 104030.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.034475 restraints weight = 72307.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.034898 restraints weight = 54105.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.035223 restraints weight = 42693.951| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 moved from start: 0.1488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 11678 Z= 0.118 Angle : 0.513 5.947 15830 Z= 0.266 Chirality : 0.040 0.174 1783 Planarity : 0.004 0.053 2030 Dihedral : 5.181 46.071 1576 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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 (0.23), residues: 1421 helix: 1.86 (0.22), residues: 579 sheet: 0.63 (0.34), residues: 202 loop : 0.15 (0.27), residues: 640 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.012 0.001 TYR A4528 PHE 0.015 0.001 PHE B 757 TRP 0.011 0.001 TRP B 660 HIS 0.005 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00246 / 0.12 (11677) covalent geometry : angle 0.51345 / 0.27 (15830) hydrogen bonds : bond 0.03154 / 2.11 ( 510) hydrogen bonds : angle 4.73633 / 3.31 ( 1413) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8852 (mtp) cc_final: 0.8452 (mtp) REVERT: B 69 MET cc_start: 0.8473 (mmp) cc_final: 0.7767 (mmm) REVERT: B 329 MET cc_start: 0.9737 (mmm) cc_final: 0.9236 (mmm) REVERT: B 479 PHE cc_start: 0.9755 (m-80) cc_final: 0.9399 (m-80) REVERT: B 492 MET cc_start: 0.9147 (tpt) cc_final: 0.8935 (tpt) REVERT: B 844 MET cc_start: 0.8701 (pmm) cc_final: 0.8088 (pmm) REVERT: C 3 ILE cc_start: 0.8821 (tp) cc_final: 0.8480 (mp) REVERT: E 1 MET cc_start: 0.8182 (ttp) cc_final: 0.7813 (tmm) REVERT: E 33 LYS cc_start: 0.8021 (mtpt) cc_final: 0.7735 (tptt) REVERT: E 74 ARG cc_start: 0.9463 (ttt-90) cc_final: 0.9251 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0747 time to fit residues: 8.0681 Evaluate side-chains 54 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 120 optimal weight: 5.9990 chunk 110 optimal weight: 5.9990 chunk 3 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 140 optimal weight: 8.9990 chunk 85 optimal weight: 0.9980 chunk 38 optimal weight: 8.9990 chunk 54 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 18 optimal weight: 0.0970 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4696 GLN B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.038755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.032894 restraints weight = 168900.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.033698 restraints weight = 103936.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034266 restraints weight = 72077.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.034681 restraints weight = 54012.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.034993 restraints weight = 42867.869| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11678 Z= 0.109 Angle : 0.502 6.191 15830 Z= 0.257 Chirality : 0.040 0.169 1783 Planarity : 0.004 0.053 2030 Dihedral : 5.126 46.652 1576 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.40 (0.23), residues: 1421 helix: 1.92 (0.22), residues: 581 sheet: 0.73 (0.35), residues: 202 loop : 0.16 (0.26), residues: 638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 74 TYR 0.007 0.001 TYR B 769 PHE 0.011 0.001 PHE B 649 TRP 0.010 0.001 TRP B 660 HIS 0.007 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (11677) covalent geometry : angle 0.50219 / 0.26 (15830) hydrogen bonds : bond 0.02852 / 1.92 ( 510) hydrogen bonds : angle 4.59290 / 3.20 ( 1413) Misc. bond : bond 0.00004 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.350 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8762 (mtp) cc_final: 0.8394 (mtp) REVERT: B 69 MET cc_start: 0.8411 (mmp) cc_final: 0.7925 (mmm) REVERT: B 479 PHE cc_start: 0.9775 (m-80) cc_final: 0.9390 (m-80) REVERT: B 844 MET cc_start: 0.8647 (pmm) cc_final: 0.7972 (pmm) REVERT: B 985 MET cc_start: 0.8709 (ppp) cc_final: 0.8363 (ppp) REVERT: C 3 ILE cc_start: 0.8844 (tp) cc_final: 0.8561 (mp) REVERT: E 1 MET cc_start: 0.8364 (ttp) cc_final: 0.7987 (tmm) REVERT: E 33 LYS cc_start: 0.8069 (mtpt) cc_final: 0.7810 (tptt) REVERT: E 74 ARG cc_start: 0.9528 (ttt-90) cc_final: 0.9320 (ttt-90) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0841 time to fit residues: 8.7650 Evaluate side-chains 52 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 127 optimal weight: 1.9990 chunk 109 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 139 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 chunk 108 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 35 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 104 optimal weight: 4.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4696 GLN B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.039346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.033519 restraints weight = 166122.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.034344 restraints weight = 101584.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 21)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.034912 restraints weight = 70209.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.035330 restraints weight = 52549.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.035659 restraints weight = 41422.983| |-----------------------------------------------------------------------------| r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 11678 Z= 0.090 Angle : 0.488 5.994 15830 Z= 0.249 Chirality : 0.040 0.156 1783 Planarity : 0.003 0.053 2030 Dihedral : 5.000 47.119 1576 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.49 (0.23), residues: 1421 helix: 2.03 (0.22), residues: 581 sheet: 0.97 (0.35), residues: 195 loop : 0.10 (0.26), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.007 0.001 TYR B 769 PHE 0.010 0.001 PHE B 649 TRP 0.007 0.001 TRP B 416 HIS 0.005 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (11677) covalent geometry : angle 0.48823 / 0.25 (15830) hydrogen bonds : bond 0.02668 / 1.79 ( 510) hydrogen bonds : angle 4.46341 / 3.11 ( 1413) Misc. bond : bond 0.00013 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8787 (mtp) cc_final: 0.8425 (mtp) REVERT: B 69 MET cc_start: 0.8446 (mmp) cc_final: 0.7965 (mmm) REVERT: B 329 MET cc_start: 0.9636 (mmt) cc_final: 0.9153 (mmm) REVERT: B 479 PHE cc_start: 0.9761 (m-80) cc_final: 0.9374 (m-80) REVERT: B 844 MET cc_start: 0.8697 (pmm) cc_final: 0.8172 (pmm) REVERT: C 3 ILE cc_start: 0.8821 (tp) cc_final: 0.8547 (mp) REVERT: E 1 MET cc_start: 0.8388 (ttp) cc_final: 0.8070 (tmm) REVERT: E 14 THR cc_start: 0.9142 (m) cc_final: 0.8893 (t) REVERT: E 33 LYS cc_start: 0.8081 (mtpt) cc_final: 0.7825 (tptt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0786 time to fit residues: 8.4598 Evaluate side-chains 52 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 13 optimal weight: 7.9990 chunk 92 optimal weight: 0.6980 chunk 36 optimal weight: 0.9980 chunk 45 optimal weight: 10.0000 chunk 58 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 115 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 111 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4696 GLN B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.039184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.033375 restraints weight = 166517.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.034194 restraints weight = 101837.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.034761 restraints weight = 70389.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.035197 restraints weight = 52659.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.035516 restraints weight = 41384.092| |-----------------------------------------------------------------------------| r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 11678 Z= 0.090 Angle : 0.490 5.951 15830 Z= 0.247 Chirality : 0.039 0.153 1783 Planarity : 0.003 0.051 2030 Dihedral : 4.926 47.041 1576 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.44 (0.23), residues: 1421 helix: 2.01 (0.22), residues: 582 sheet: 0.57 (0.35), residues: 212 loop : 0.17 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 869 TYR 0.007 0.001 TYR B 769 PHE 0.009 0.001 PHE B 649 TRP 0.009 0.001 TRP B 660 HIS 0.006 0.001 HIS B1001 Details of bonding type rmsd/Z covalent geometry : bond 0.00190 / 0.09 (11677) covalent geometry : angle 0.48987 / 0.25 (15830) hydrogen bonds : bond 0.02585 / 1.74 ( 510) hydrogen bonds : angle 4.40904 / 3.06 ( 1413) Misc. bond : bond 0.00001 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.511 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8793 (mtp) cc_final: 0.8410 (mtp) REVERT: A 4626 PHE cc_start: 0.9054 (m-80) cc_final: 0.8853 (m-80) REVERT: B 69 MET cc_start: 0.8490 (mmp) cc_final: 0.7971 (mmm) REVERT: B 479 PHE cc_start: 0.9757 (m-80) cc_final: 0.9361 (m-80) REVERT: B 492 MET cc_start: 0.9125 (tpt) cc_final: 0.8922 (tpt) REVERT: B 844 MET cc_start: 0.8663 (pmm) cc_final: 0.7968 (pmm) REVERT: B 985 MET cc_start: 0.8714 (ppp) cc_final: 0.8353 (ppp) REVERT: C 3 ILE cc_start: 0.8968 (tp) cc_final: 0.8550 (mp) REVERT: E 1 MET cc_start: 0.8471 (ttp) cc_final: 0.8161 (tmm) REVERT: E 14 THR cc_start: 0.9138 (m) cc_final: 0.8877 (t) REVERT: E 33 LYS cc_start: 0.8105 (mtpt) cc_final: 0.7744 (tptt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.0664 time to fit residues: 7.2681 Evaluate side-chains 53 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 126 optimal weight: 7.9990 chunk 8 optimal weight: 0.8980 chunk 137 optimal weight: 0.0060 chunk 79 optimal weight: 0.4980 chunk 83 optimal weight: 9.9990 chunk 2 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 58 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 85 optimal weight: 0.0470 overall best weight: 1.4896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.039166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.033389 restraints weight = 165823.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 18)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.034208 restraints weight = 101318.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.034766 restraints weight = 69847.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.035193 restraints weight = 52505.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.035520 restraints weight = 41188.685| |-----------------------------------------------------------------------------| r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 11678 Z= 0.089 Angle : 0.491 5.838 15830 Z= 0.248 Chirality : 0.039 0.149 1783 Planarity : 0.003 0.049 2030 Dihedral : 4.937 47.111 1576 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.46 (0.23), residues: 1421 helix: 2.02 (0.22), residues: 582 sheet: 0.58 (0.35), residues: 212 loop : 0.19 (0.27), residues: 627 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.006 0.001 TYR B 769 PHE 0.009 0.001 PHE B 649 TRP 0.009 0.001 TRP B 660 HIS 0.004 0.001 HIS B 858 Details of bonding type rmsd/Z covalent geometry : bond 0.00191 / 0.09 (11677) covalent geometry : angle 0.49141 / 0.25 (15830) hydrogen bonds : bond 0.02551 / 1.72 ( 510) hydrogen bonds : angle 4.36584 / 3.03 ( 1413) Misc. bond : bond 0.00009 / 0.00 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8694 (mtp) cc_final: 0.8360 (mtp) REVERT: A 4626 PHE cc_start: 0.9080 (m-80) cc_final: 0.8867 (m-80) REVERT: B 69 MET cc_start: 0.8609 (mmp) cc_final: 0.8058 (mmm) REVERT: B 329 MET cc_start: 0.9582 (mmt) cc_final: 0.9138 (mmm) REVERT: B 479 PHE cc_start: 0.9751 (m-80) cc_final: 0.9342 (m-80) REVERT: B 492 MET cc_start: 0.9126 (tpt) cc_final: 0.8920 (tpt) REVERT: B 844 MET cc_start: 0.8682 (pmm) cc_final: 0.8093 (pmm) REVERT: C 3 ILE cc_start: 0.8822 (tp) cc_final: 0.8544 (mp) REVERT: C 4 PHE cc_start: 0.8407 (m-80) cc_final: 0.7707 (m-80) REVERT: E 1 MET cc_start: 0.8524 (ttp) cc_final: 0.8247 (tmm) REVERT: E 14 THR cc_start: 0.9163 (m) cc_final: 0.8902 (t) REVERT: E 33 LYS cc_start: 0.8093 (mtpt) cc_final: 0.7866 (tptt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0730 time to fit residues: 7.9471 Evaluate side-chains 55 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 19 optimal weight: 9.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 20.0000 chunk 119 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 86 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 58 optimal weight: 1.9990 chunk 137 optimal weight: 3.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A4536 GLN A4758 HIS B 171 ASN ** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.037387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.031681 restraints weight = 172029.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.032464 restraints weight = 105221.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.033010 restraints weight = 72863.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.033416 restraints weight = 54661.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.033726 restraints weight = 43246.965| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 11678 Z= 0.138 Angle : 0.535 7.993 15830 Z= 0.273 Chirality : 0.039 0.148 1783 Planarity : 0.004 0.047 2030 Dihedral : 5.125 51.691 1576 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.36 (0.23), residues: 1421 helix: 1.98 (0.22), residues: 583 sheet: 0.51 (0.35), residues: 209 loop : 0.11 (0.27), residues: 629 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG E 74 TYR 0.009 0.001 TYR A4705 PHE 0.016 0.001 PHE B1028 TRP 0.011 0.001 TRP B 660 HIS 0.008 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00287 / 0.14 (11677) covalent geometry : angle 0.53476 / 0.27 (15830) hydrogen bonds : bond 0.02768 / 1.85 ( 510) hydrogen bonds : angle 4.52199 / 3.14 ( 1413) Misc. bond : bond 0.00016 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8736 (mtp) cc_final: 0.8479 (mtt) REVERT: B 69 MET cc_start: 0.8729 (mmp) cc_final: 0.8181 (mmm) REVERT: B 329 MET cc_start: 0.9704 (mmm) cc_final: 0.9210 (mmm) REVERT: B 479 PHE cc_start: 0.9729 (m-80) cc_final: 0.9330 (m-80) REVERT: B 844 MET cc_start: 0.8673 (pmm) cc_final: 0.8119 (pmm) REVERT: B 904 LEU cc_start: 0.9839 (tp) cc_final: 0.9481 (tt) REVERT: B 907 LEU cc_start: 0.9804 (tp) cc_final: 0.9582 (tp) REVERT: B 908 GLU cc_start: 0.9448 (mm-30) cc_final: 0.9025 (mm-30) REVERT: B 985 MET cc_start: 0.8789 (ppp) cc_final: 0.8450 (ppp) REVERT: C 4 PHE cc_start: 0.8375 (m-80) cc_final: 0.7671 (m-80) REVERT: E 1 MET cc_start: 0.8698 (ttp) cc_final: 0.8444 (tmm) REVERT: E 33 LYS cc_start: 0.8088 (mtpt) cc_final: 0.7848 (tptt) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.0721 time to fit residues: 7.9283 Evaluate side-chains 49 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 63 optimal weight: 8.9990 chunk 133 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 97 optimal weight: 6.9990 chunk 27 optimal weight: 3.9990 chunk 113 optimal weight: 2.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 5.9990 chunk 109 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN ** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.037703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.032060 restraints weight = 167843.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.032837 restraints weight = 102565.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.033392 restraints weight = 70857.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.033749 restraints weight = 52888.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.034058 restraints weight = 42634.325| |-----------------------------------------------------------------------------| r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 11678 Z= 0.112 Angle : 0.516 6.084 15830 Z= 0.264 Chirality : 0.040 0.169 1783 Planarity : 0.003 0.047 2030 Dihedral : 5.089 52.872 1576 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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: 1.35 (0.23), residues: 1421 helix: 1.96 (0.22), residues: 575 sheet: 0.68 (0.35), residues: 202 loop : 0.07 (0.26), residues: 644 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 54 TYR 0.007 0.001 TYR B 769 PHE 0.010 0.001 PHE A4598 TRP 0.011 0.001 TRP B 660 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00233 / 0.11 (11677) covalent geometry : angle 0.51603 / 0.26 (15830) hydrogen bonds : bond 0.02669 / 1.77 ( 510) hydrogen bonds : angle 4.55855 / 3.15 ( 1413) Misc. bond : bond 0.00010 / 0.01 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8778 (mtp) cc_final: 0.8501 (mtt) REVERT: A 4609 MET cc_start: 0.9428 (mmp) cc_final: 0.8507 (mmp) REVERT: A 4632 PHE cc_start: 0.9585 (m-80) cc_final: 0.9069 (m-80) REVERT: B 69 MET cc_start: 0.8597 (mmp) cc_final: 0.8144 (mmm) REVERT: B 329 MET cc_start: 0.9722 (mmm) cc_final: 0.9247 (mmm) REVERT: B 479 PHE cc_start: 0.9755 (m-80) cc_final: 0.9344 (m-80) REVERT: B 844 MET cc_start: 0.8731 (pmm) cc_final: 0.8165 (pmm) REVERT: B 904 LEU cc_start: 0.9850 (tp) cc_final: 0.9493 (tt) REVERT: B 908 GLU cc_start: 0.9483 (mm-30) cc_final: 0.9062 (mm-30) REVERT: C 4 PHE cc_start: 0.8461 (m-80) cc_final: 0.7761 (m-80) outliers start: 0 outliers final: 0 residues processed: 69 average time/residue: 0.0602 time to fit residues: 6.7713 Evaluate side-chains 48 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 121 optimal weight: 9.9990 chunk 107 optimal weight: 0.5980 chunk 111 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 77 optimal weight: 8.9990 chunk 123 optimal weight: 9.9990 chunk 140 optimal weight: 4.9990 chunk 131 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN ** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.038173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.032424 restraints weight = 168431.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.033213 restraints weight = 102133.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.033781 restraints weight = 70186.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.034199 restraints weight = 52144.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.034504 restraints weight = 40882.297| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 11678 Z= 0.097 Angle : 0.519 7.381 15830 Z= 0.263 Chirality : 0.040 0.143 1783 Planarity : 0.003 0.048 2030 Dihedral : 5.059 53.799 1576 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.23), residues: 1421 helix: 1.92 (0.22), residues: 581 sheet: 0.53 (0.35), residues: 209 loop : 0.13 (0.27), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 74 TYR 0.007 0.001 TYR B 769 PHE 0.010 0.001 PHE B1028 TRP 0.011 0.001 TRP B 660 HIS 0.004 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00207 / 0.10 (11677) covalent geometry : angle 0.51919 / 0.26 (15830) hydrogen bonds : bond 0.02623 / 1.74 ( 510) hydrogen bonds : angle 4.50791 / 3.11 ( 1413) Misc. bond : bond 0.00010 / 0.01 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2842 Ramachandran restraints generated. 1421 Oldfield, 0 Emsley, 1421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 4532 MET cc_start: 0.8716 (mtp) cc_final: 0.8435 (mtt) REVERT: B 69 MET cc_start: 0.8558 (mmp) cc_final: 0.8058 (mmm) REVERT: B 479 PHE cc_start: 0.9757 (m-80) cc_final: 0.9337 (m-80) REVERT: B 844 MET cc_start: 0.8725 (pmm) cc_final: 0.8160 (pmm) REVERT: B 904 LEU cc_start: 0.9845 (tp) cc_final: 0.9500 (tt) REVERT: B 908 GLU cc_start: 0.9495 (mm-30) cc_final: 0.9068 (mm-30) REVERT: B 985 MET cc_start: 0.8869 (ppp) cc_final: 0.8463 (ppp) REVERT: C 4 PHE cc_start: 0.8492 (m-80) cc_final: 0.7795 (m-80) REVERT: E 1 MET cc_start: 0.8967 (tmm) cc_final: 0.8471 (tmm) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.0665 time to fit residues: 7.1802 Evaluate side-chains 50 residues out of total 1266 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 141 random chunks: chunk 57 optimal weight: 0.6980 chunk 132 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 104 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 105 optimal weight: 1.9990 overall best weight: 2.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 171 ASN ** B 599 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.036400 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.030900 restraints weight = 173747.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.031666 restraints weight = 105425.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.032210 restraints weight = 72727.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.032616 restraints weight = 54620.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.032910 restraints weight = 42881.999| |-----------------------------------------------------------------------------| r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8259 moved from start: 0.3364 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11678 Z= 0.136 Angle : 0.541 6.685 15830 Z= 0.277 Chirality : 0.040 0.145 1783 Planarity : 0.004 0.047 2030 Dihedral : 5.223 58.044 1576 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.76 % Cis-general : 0.07 % 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 (0.23), residues: 1421 helix: 1.85 (0.22), residues: 582 sheet: 0.52 (0.36), residues: 208 loop : 0.08 (0.27), residues: 631 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 54 TYR 0.008 0.001 TYR A4705 PHE 0.014 0.001 PHE B1028 TRP 0.012 0.001 TRP B 660 HIS 0.007 0.001 HIS C 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 (11677) covalent geometry : angle 0.54106 / 0.28 (15830) hydrogen bonds : bond 0.02811 / 1.87 ( 510) hydrogen bonds : angle 4.60000 / 3.17 ( 1413) Misc. bond : bond 0.00014 / 0.01 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.25 seconds wall clock time: 24 minutes 6.61 seconds (1446.61 seconds total)