Starting phenix.real_space_refine on Fri Aug 7 11:22:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ihe_52866/08_2026/9ihe_52866.map" } resolution = 2.95 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= 0.000 sd= 1.000 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: 6 Type Number sf(0) Gaussians Fe 2 7.16 5 P 290 5.49 5 S 70 5.16 5 C 12368 2.51 5 N 3902 2.21 5 O 4437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 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: 21069 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 795 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 825 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 735 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2955 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "L" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "M" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 806 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 9, 'TRANS': 90} Chain: "N" Number of atoms: 3670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3670 Classifications: {'peptide': 457} Link IDs: {'PCIS': 3, 'PTRANS': 33, 'TRANS': 420} Chain: "L" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "N" Number of atoms: 85 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 85 Unusual residues: {'HEM': 1, 'NAG': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 4.31, per 1000 atoms: 0.20 Number of scatterers: 21069 At special positions: 0 Unit cell: (119.68, 120.36, 169.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 2 26.01 S 70 16.00 P 290 15.00 O 4437 8.00 N 3902 7.00 C 12368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS L 221 " - pdb=" SG CYS L 232 " distance=2.03 Simple disulfide: pdb=" SG CYS L 440 " - pdb=" SG CYS L 497 " distance=2.04 Simple disulfide: pdb=" SG CYS L 538 " - pdb=" SG CYS L 564 " distance=2.03 Simple disulfide: pdb=" SG CYS N 221 " - pdb=" SG CYS N 232 " distance=2.03 Simple disulfide: pdb=" SG CYS N 440 " - pdb=" SG CYS N 497 " distance=2.03 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.96 Conformation dependent library (CDL) restraints added in 748.8 milliseconds 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3510 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 19 sheets defined 56.0% alpha, 3.0% beta 134 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 2.64 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 4.097A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.565A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.546A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.792A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.062A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 3.502A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.704A pdb=" N VAL D 38 " --> pdb=" O TYR D 34 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.563A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LYS D 117 " --> pdb=" O LYS D 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.541A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.524A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.827A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.518A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.670A pdb=" N VAL H 38 " --> pdb=" O TYR H 34 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.738A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 68 Processing helix chain 'K' and resid 72 through 76 removed outlier: 3.804A pdb=" N GLN K 75 " --> pdb=" O PRO K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 84 through 98 Processing helix chain 'L' and resid 173 through 178 removed outlier: 3.649A pdb=" N TYR L 177 " --> pdb=" O ALA L 173 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY L 178 " --> pdb=" O SER L 174 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 173 through 178' Processing helix chain 'L' and resid 180 through 188 removed outlier: 3.594A pdb=" N ARG L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing helix chain 'L' and resid 219 through 225 removed outlier: 3.805A pdb=" N ASN L 225 " --> pdb=" O CYS L 221 " (cutoff:3.500A) Processing helix chain 'L' and resid 243 through 268 Processing helix chain 'L' and resid 272 through 302 removed outlier: 5.362A pdb=" N LEU L 297 " --> pdb=" O TYR L 293 " (cutoff:3.500A) Proline residue: L 298 - end of helix Processing helix chain 'L' and resid 302 through 310 Processing helix chain 'L' and resid 327 through 332 Processing helix chain 'L' and resid 333 through 338 Processing helix chain 'L' and resid 362 through 364 No H-bonds generated for 'chain 'L' and resid 362 through 364' Processing helix chain 'L' and resid 368 through 373 removed outlier: 3.667A pdb=" N VAL L 372 " --> pdb=" O SER L 368 " (cutoff:3.500A) Processing helix chain 'L' and resid 377 through 386 Processing helix chain 'L' and resid 400 through 405 Processing helix chain 'L' and resid 416 through 428 Processing helix chain 'L' and resid 432 through 441 Processing helix chain 'L' and resid 447 through 456 Processing helix chain 'L' and resid 458 through 469 Processing helix chain 'L' and resid 470 through 474 removed outlier: 3.536A pdb=" N ILE L 474 " --> pdb=" O PRO L 471 " (cutoff:3.500A) Processing helix chain 'L' and resid 475 through 483 Processing helix chain 'L' and resid 492 through 510 removed outlier: 3.505A pdb=" N ASP L 510 " --> pdb=" O LEU L 506 " (cutoff:3.500A) Processing helix chain 'L' and resid 521 through 529 Processing helix chain 'L' and resid 532 through 540 Processing helix chain 'L' and resid 571 through 576 removed outlier: 4.271A pdb=" N SER L 574 " --> pdb=" O ASN L 571 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ARG L 576 " --> pdb=" O ALA L 573 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 68 Processing helix chain 'M' and resid 72 through 76 Processing helix chain 'M' and resid 84 through 98 Processing helix chain 'N' and resid 180 through 187 Processing helix chain 'N' and resid 219 through 225 removed outlier: 4.242A pdb=" N LEU N 223 " --> pdb=" O ASP N 219 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N THR N 224 " --> pdb=" O PRO N 220 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ASN N 225 " --> pdb=" O CYS N 221 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 219 through 225' Processing helix chain 'N' and resid 243 through 268 Processing helix chain 'N' and resid 272 through 302 removed outlier: 5.353A pdb=" N LEU N 297 " --> pdb=" O TYR N 293 " (cutoff:3.500A) Proline residue: N 298 - end of helix Processing helix chain 'N' and resid 302 through 310 Processing helix chain 'N' and resid 327 through 332 Processing helix chain 'N' and resid 333 through 338 Processing helix chain 'N' and resid 362 through 364 No H-bonds generated for 'chain 'N' and resid 362 through 364' Processing helix chain 'N' and resid 368 through 373 removed outlier: 3.578A pdb=" N VAL N 372 " --> pdb=" O SER N 368 " (cutoff:3.500A) Processing helix chain 'N' and resid 377 through 386 Processing helix chain 'N' and resid 399 through 405 Processing helix chain 'N' and resid 416 through 428 Processing helix chain 'N' and resid 432 through 441 Processing helix chain 'N' and resid 447 through 456 Processing helix chain 'N' and resid 457 through 469 removed outlier: 3.556A pdb=" N ALA N 461 " --> pdb=" O ASN N 457 " (cutoff:3.500A) Processing helix chain 'N' and resid 470 through 474 Processing helix chain 'N' and resid 475 through 483 Processing helix chain 'N' and resid 492 through 509 Processing helix chain 'N' and resid 521 through 529 Processing helix chain 'N' and resid 532 through 541 Processing helix chain 'N' and resid 571 through 576 removed outlier: 4.248A pdb=" N SER N 574 " --> pdb=" O ASN N 571 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG N 576 " --> pdb=" O ALA N 573 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.959A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.117A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.667A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.083A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.162A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.631A pdb=" N ARG K 27 " --> pdb=" O ASN L 165 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 78 through 83 removed outlier: 4.368A pdb=" N ALA L 389 " --> pdb=" O ASP K 79 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'L' and resid 342 through 344 Processing sheet with id=AB5, first strand: chain 'L' and resid 546 through 547 Processing sheet with id=AB6, first strand: chain 'M' and resid 27 through 28 removed outlier: 3.522A pdb=" N ARG M 27 " --> pdb=" O ASN N 165 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 78 through 83 removed outlier: 4.130A pdb=" N ALA N 389 " --> pdb=" O ASP M 79 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 188 through 189 removed outlier: 4.568A pdb=" N LEU N 196 " --> pdb=" O ASN N 189 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'N' and resid 342 through 344 Processing sheet with id=AC1, first strand: chain 'N' and resid 546 through 547 702 hydrogen bonds defined for protein. 2046 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 344 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 134 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 4.76 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.38: 8167 1.38 - 1.55: 13230 1.55 - 1.72: 584 1.72 - 1.88: 116 1.88 - 2.05: 8 Bond restraints: 22105 Sorted by residual: bond pdb=" C3' DC J -21 " pdb=" C2' DC J -21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C1' DC J 35 " pdb=" N1 DC J 35 " ideal model delta sigma weight residual 1.468 1.513 -0.045 1.40e-02 5.10e+03 1.03e+01 bond pdb=" C3' DA J 63 " pdb=" C2' DA J 63 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.13e+00 bond pdb=" C3' DT J 13 " pdb=" C2' DT J 13 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.80e+00 bond pdb=" C3' DA I -30 " pdb=" C2' DA I -30 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 8.65e+00 ... (remaining 22100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 29645 1.49 - 2.99: 1412 2.99 - 4.48: 105 4.48 - 5.98: 24 5.98 - 7.47: 5 Bond angle restraints: 31191 Sorted by residual: angle pdb=" O4' DC I -48 " pdb=" C4' DC I -48 " pdb=" C3' DC I -48 " ideal model delta sigma weight residual 106.00 103.07 2.93 6.00e-01 2.78e+00 2.38e+01 angle pdb=" O4' DC J -48 " pdb=" C4' DC J -48 " pdb=" C3' DC J -48 " ideal model delta sigma weight residual 106.00 103.29 2.71 6.00e-01 2.78e+00 2.04e+01 angle pdb=" N3 DT I 9 " pdb=" C4 DT I 9 " pdb=" O4 DT I 9 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 angle pdb=" N3 DT I -32 " pdb=" C4 DT I -32 " pdb=" O4 DT I -32 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 angle pdb=" N3 DT J 38 " pdb=" C4 DT J 38 " pdb=" O4 DT J 38 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.94e+01 ... (remaining 31186 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.02: 10987 35.02 - 70.04: 1668 70.04 - 105.06: 26 105.06 - 140.08: 2 140.08 - 175.10: 6 Dihedral angle restraints: 12689 sinusoidal: 7261 harmonic: 5428 Sorted by residual: dihedral pdb=" C4' DA J 32 " pdb=" C3' DA J 32 " pdb=" O3' DA J 32 " pdb=" P DC J 33 " ideal model delta sinusoidal sigma weight residual 220.00 44.90 175.10 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DA J -31 " pdb=" C3' DA J -31 " pdb=" O3' DA J -31 " pdb=" P DG J -30 " ideal model delta sinusoidal sigma weight residual 220.00 60.63 159.37 1 3.50e+01 8.16e-04 1.52e+01 dihedral pdb=" C4' DC J 35 " pdb=" C3' DC J 35 " pdb=" O3' DC J 35 " pdb=" P DC J 36 " ideal model delta sinusoidal sigma weight residual 220.00 62.75 157.25 1 3.50e+01 8.16e-04 1.51e+01 ... (remaining 12686 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1972 0.031 - 0.063: 978 0.063 - 0.094: 327 0.094 - 0.125: 167 0.125 - 0.156: 15 Chirality restraints: 3459 Sorted by residual: chirality pdb=" C3' DA J 32 " pdb=" C4' DA J 32 " pdb=" O3' DA J 32 " pdb=" C2' DA J 32 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" C3' DA J -31 " pdb=" C4' DA J -31 " pdb=" O3' DA J -31 " pdb=" C2' DA J -31 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.57e-01 chirality pdb=" P DC J 36 " pdb=" OP1 DC J 36 " pdb=" OP2 DC J 36 " pdb=" O5' DC J 36 " both_signs ideal model delta sigma weight residual True 2.34 -2.48 -0.15 2.00e-01 2.50e+01 5.43e-01 ... (remaining 3456 not shown) Planarity restraints: 3007 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER D 109 " 0.009 2.00e-02 2.50e+03 1.84e-02 3.37e+00 pdb=" C SER D 109 " -0.032 2.00e-02 2.50e+03 pdb=" O SER D 109 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU D 110 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 110 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C GLU H 110 " -0.031 2.00e-02 2.50e+03 pdb=" O GLU H 110 " 0.012 2.00e-02 2.50e+03 pdb=" N GLY H 111 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 108 " -0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C VAL H 108 " 0.030 2.00e-02 2.50e+03 pdb=" O VAL H 108 " -0.011 2.00e-02 2.50e+03 pdb=" N SER H 109 " -0.010 2.00e-02 2.50e+03 ... (remaining 3004 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 555 2.68 - 3.24: 18180 3.24 - 3.79: 35862 3.79 - 4.35: 49080 4.35 - 4.90: 74610 Nonbonded interactions: 178287 Sorted by model distance: nonbonded pdb=" OD2 ASP C 90 " pdb=" NH2 ARG L 307 " model vdw 2.129 3.120 nonbonded pdb=" OD2 ASP G 90 " pdb=" NH2 ARG N 307 " model vdw 2.164 3.120 nonbonded pdb=" OH TYR L 350 " pdb=" O THR L 545 " model vdw 2.203 3.040 nonbonded pdb=" OE1 GLU E 73 " pdb=" ND2 ASN F 25 " model vdw 2.230 3.120 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.246 3.040 ... (remaining 178282 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 'A' and resid 39 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and resid 11 through 117) selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'M' } ncs_group { reference = chain 'L' selection = chain 'N' } 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: 6.110 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: 0.510 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 22.260 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.060 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:6.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 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 : 0.008 0.644 22112 Z= 0.445 Angle : 0.670 7.469 31201 Z= 0.543 Chirality : 0.044 0.156 3459 Planarity : 0.005 0.055 3007 Dihedral : 24.940 175.095 9164 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.43 % Allowed : 25.40 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.02 (0.19), residues: 1846 helix: 1.59 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -0.24 (0.20), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG N 349 TYR 0.010 0.001 TYR L 177 PHE 0.010 0.001 PHE K 86 TRP 0.007 0.001 TRP M 89 HIS 0.002 0.001 HIS L 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00577 / 0.44 (22105) covalent geometry : angle 0.67036 / 0.54 (31191) SS BOND : bond 0.00283 / 0.17 ( 5) SS BOND : angle 0.60935 / 0.38 ( 10) hydrogen bonds : bond 0.12574 / 8.26 ( 1046) hydrogen bonds : angle 5.07056 / 3.61 ( 2730) Misc. bond : bond 0.64040 / 44.23 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 187 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: C 73 ASN cc_start: 0.8398 (t0) cc_final: 0.7817 (t0) REVERT: D 56 MET cc_start: 0.8775 (tpp) cc_final: 0.8539 (mmm) REVERT: E 56 LYS cc_start: 0.8896 (mtpt) cc_final: 0.8553 (mtmm) REVERT: E 79 LYS cc_start: 0.8804 (tttm) cc_final: 0.8594 (tttt) REVERT: E 122 LYS cc_start: 0.8137 (ptmt) cc_final: 0.7677 (pttt) REVERT: F 93 GLN cc_start: 0.8745 (OUTLIER) cc_final: 0.7813 (mm-40) REVERT: G 15 LYS cc_start: 0.8643 (mttt) cc_final: 0.8149 (mtpt) REVERT: G 95 LYS cc_start: 0.8759 (tttt) cc_final: 0.8266 (ttmt) REVERT: G 99 ARG cc_start: 0.8652 (mtp180) cc_final: 0.7809 (mmm160) REVERT: G 108 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8562 (mp) REVERT: H 68 GLU cc_start: 0.7429 (OUTLIER) cc_final: 0.7000 (tt0) REVERT: K 7 TYR cc_start: 0.8613 (m-80) cc_final: 0.8274 (m-80) REVERT: K 56 PHE cc_start: 0.8355 (m-80) cc_final: 0.8053 (m-80) REVERT: L 216 LEU cc_start: 0.7561 (mt) cc_final: 0.7210 (mp) REVERT: L 229 ARG cc_start: 0.7919 (tmm160) cc_final: 0.7651 (tmm160) REVERT: M 67 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7528 (mp0) REVERT: N 205 ASP cc_start: 0.7647 (t0) cc_final: 0.7250 (t0) REVERT: N 530 GLN cc_start: 0.8950 (OUTLIER) cc_final: 0.8438 (mm110) outliers start: 23 outliers final: 15 residues processed: 204 average time/residue: 0.7118 time to fit residues: 160.8565 Evaluate side-chains 200 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 19 SER Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 530 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 98 optimal weight: 20.0000 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.0970 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 1.9990 chunk 200 optimal weight: 0.7980 chunk 77 optimal weight: 8.9990 chunk 122 optimal weight: 8.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN K 80 GLN K 88 GLN L 122 GLN L 133 ASN M 54 ASN M 75 GLN N 133 ASN N 140 GLN N 257 HIS N 330 ASN N 421 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.139039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.092950 restraints weight = 26903.640| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.62 r_work: 0.2921 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.0540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.239 22112 Z= 0.150 Angle : 0.612 17.277 31201 Z= 0.326 Chirality : 0.044 0.269 3459 Planarity : 0.004 0.045 3007 Dihedral : 27.211 178.350 5442 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 3.61 % Allowed : 22.29 % Favored : 74.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.26 (0.20), residues: 1846 helix: 1.77 (0.17), residues: 985 sheet: None (None), residues: 0 loop : -0.21 (0.20), residues: 861 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 70 TYR 0.011 0.001 TYR L 177 PHE 0.009 0.001 PHE K 86 TRP 0.008 0.001 TRP N 436 HIS 0.003 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.15 (22105) covalent geometry : angle 0.61233 / 0.33 (31191) SS BOND : bond 0.00324 / 0.20 ( 5) SS BOND : angle 0.71064 / 0.47 ( 10) hydrogen bonds : bond 0.05286 / 3.59 ( 1046) hydrogen bonds : angle 3.80505 / 2.74 ( 2730) Misc. bond : bond 0.23543 / 16.25 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 249 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 191 time to evaluate : 0.692 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8163 (mtm) REVERT: C 73 ASN cc_start: 0.7936 (t0) cc_final: 0.7400 (t0) REVERT: E 42 ARG cc_start: 0.7716 (mtt-85) cc_final: 0.7457 (mmt90) REVERT: E 56 LYS cc_start: 0.8850 (mtpt) cc_final: 0.8541 (mtmm) REVERT: E 79 LYS cc_start: 0.8829 (tttm) cc_final: 0.8542 (tttt) REVERT: E 115 LYS cc_start: 0.8516 (OUTLIER) cc_final: 0.8141 (mtpt) REVERT: E 122 LYS cc_start: 0.8182 (ptmt) cc_final: 0.7694 (pttt) REVERT: G 15 LYS cc_start: 0.8285 (mttt) cc_final: 0.7715 (mtpt) REVERT: G 95 LYS cc_start: 0.8823 (tttt) cc_final: 0.8338 (ttmt) REVERT: G 99 ARG cc_start: 0.8528 (mtp180) cc_final: 0.7829 (mmm160) REVERT: H 32 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.8048 (pt0) REVERT: H 68 GLU cc_start: 0.7690 (OUTLIER) cc_final: 0.7298 (tt0) REVERT: K 7 TYR cc_start: 0.8632 (m-80) cc_final: 0.8151 (m-80) REVERT: K 56 PHE cc_start: 0.8130 (m-80) cc_final: 0.7814 (m-80) REVERT: L 216 LEU cc_start: 0.7470 (mt) cc_final: 0.7102 (mp) REVERT: L 229 ARG cc_start: 0.7930 (tmm160) cc_final: 0.7670 (tmm160) REVERT: M 81 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8250 (mm-30) REVERT: N 205 ASP cc_start: 0.7575 (t0) cc_final: 0.7151 (t0) REVERT: N 349 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.8080 (ttm110) outliers start: 58 outliers final: 19 residues processed: 229 average time/residue: 0.7373 time to fit residues: 187.1181 Evaluate side-chains 208 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 183 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 448 VAL Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 567 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 177 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 172 optimal weight: 8.9990 chunk 194 optimal weight: 8.9990 chunk 135 optimal weight: 9.9990 chunk 0 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 12 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 208 optimal weight: 7.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 27 GLN D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 122 GLN L 133 ASN M 54 ASN M 75 GLN M 88 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.135629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.089616 restraints weight = 26945.655| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 1.67 r_work: 0.2847 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2698 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.0688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.205 22112 Z= 0.266 Angle : 0.665 16.524 31201 Z= 0.349 Chirality : 0.048 0.292 3459 Planarity : 0.005 0.043 3007 Dihedral : 27.412 175.419 5418 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 4.92 % Allowed : 21.61 % Favored : 73.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 0.97 (0.19), residues: 1846 helix: 1.57 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.43 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 70 TYR 0.011 0.002 TYR F 51 PHE 0.012 0.002 PHE H 62 TRP 0.007 0.001 TRP N 436 HIS 0.005 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.27 (22105) covalent geometry : angle 0.66470 / 0.35 (31191) SS BOND : bond 0.00476 / 0.27 ( 5) SS BOND : angle 0.67573 / 0.43 ( 10) hydrogen bonds : bond 0.06355 / 4.29 ( 1046) hydrogen bonds : angle 3.80332 / 2.76 ( 2730) Misc. bond : bond 0.19786 / 13.70 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 188 time to evaluate : 0.591 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8292 (mtm) REVERT: C 73 ASN cc_start: 0.7935 (t0) cc_final: 0.7418 (t0) REVERT: C 92 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8302 (mp0) REVERT: E 42 ARG cc_start: 0.7761 (mtt-85) cc_final: 0.7438 (mmt90) REVERT: E 79 LYS cc_start: 0.8888 (tttm) cc_final: 0.8664 (tttt) REVERT: E 115 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8201 (mtpt) REVERT: E 122 LYS cc_start: 0.8306 (ptmt) cc_final: 0.7771 (pttt) REVERT: F 93 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8016 (mm-40) REVERT: G 15 LYS cc_start: 0.8395 (mttt) cc_final: 0.7788 (mtpt) REVERT: G 95 LYS cc_start: 0.8839 (tttt) cc_final: 0.8383 (ttmt) REVERT: G 99 ARG cc_start: 0.8563 (mtp180) cc_final: 0.7854 (mmm160) REVERT: H 68 GLU cc_start: 0.7800 (OUTLIER) cc_final: 0.7417 (tt0) REVERT: K 7 TYR cc_start: 0.8685 (m-80) cc_final: 0.8174 (m-80) REVERT: K 56 PHE cc_start: 0.8144 (m-80) cc_final: 0.7845 (m-80) REVERT: L 216 LEU cc_start: 0.7503 (mt) cc_final: 0.7107 (mp) REVERT: L 229 ARG cc_start: 0.7949 (tmm160) cc_final: 0.7621 (tmm160) REVERT: L 250 HIS cc_start: 0.8473 (OUTLIER) cc_final: 0.8021 (m90) REVERT: M 81 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8249 (mm-30) REVERT: N 205 ASP cc_start: 0.7543 (t0) cc_final: 0.7119 (t0) REVERT: N 349 ARG cc_start: 0.8288 (OUTLIER) cc_final: 0.8010 (ttm110) outliers start: 79 outliers final: 34 residues processed: 246 average time/residue: 0.7339 time to fit residues: 201.2994 Evaluate side-chains 228 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 186 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 30 VAL Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain M residue 81 GLU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 262 THR Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 478 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 28 optimal weight: 0.8980 chunk 135 optimal weight: 7.9990 chunk 199 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 188 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 191 optimal weight: 0.9990 chunk 177 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 4 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN K 80 GLN K 88 GLN L 133 ASN M 75 GLN N 140 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.138644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.092597 restraints weight = 26837.839| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.58 r_work: 0.2913 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.0742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.235 22112 Z= 0.134 Angle : 0.587 11.435 31201 Z= 0.316 Chirality : 0.044 0.269 3459 Planarity : 0.004 0.036 3007 Dihedral : 27.349 177.474 5418 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.11 % Allowed : 23.47 % Favored : 73.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.32 (0.20), residues: 1846 helix: 1.86 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.26 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 70 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE K 86 TRP 0.010 0.001 TRP N 436 HIS 0.002 0.000 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.13 (22105) covalent geometry : angle 0.58664 / 0.32 (31191) SS BOND : bond 0.00944 / 0.46 ( 5) SS BOND : angle 0.78945 / 0.51 ( 10) hydrogen bonds : bond 0.05009 / 3.40 ( 1046) hydrogen bonds : angle 3.59829 / 2.61 ( 2730) Misc. bond : bond 0.22915 / 15.80 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 189 time to evaluate : 0.713 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8922 (OUTLIER) cc_final: 0.8156 (mtm) REVERT: C 73 ASN cc_start: 0.7871 (t0) cc_final: 0.7381 (t0) REVERT: E 42 ARG cc_start: 0.7721 (mtt-85) cc_final: 0.7416 (mmt90) REVERT: E 79 LYS cc_start: 0.8846 (tttm) cc_final: 0.8630 (tttt) REVERT: E 122 LYS cc_start: 0.8184 (ptmt) cc_final: 0.7684 (pttt) REVERT: G 15 LYS cc_start: 0.8330 (mttt) cc_final: 0.7748 (mtpt) REVERT: G 95 LYS cc_start: 0.8820 (tttt) cc_final: 0.8350 (ttmt) REVERT: G 99 ARG cc_start: 0.8551 (mtp180) cc_final: 0.7841 (mmm160) REVERT: G 108 LEU cc_start: 0.9009 (OUTLIER) cc_final: 0.8492 (mp) REVERT: H 68 GLU cc_start: 0.7714 (OUTLIER) cc_final: 0.7376 (tt0) REVERT: K 7 TYR cc_start: 0.8652 (m-80) cc_final: 0.8133 (m-80) REVERT: K 56 PHE cc_start: 0.8144 (m-80) cc_final: 0.7803 (m-80) REVERT: L 216 LEU cc_start: 0.7479 (mt) cc_final: 0.7095 (mp) REVERT: L 229 ARG cc_start: 0.7965 (tmm160) cc_final: 0.7652 (tmm160) REVERT: L 250 HIS cc_start: 0.8423 (OUTLIER) cc_final: 0.7871 (m90) REVERT: N 205 ASP cc_start: 0.7540 (t0) cc_final: 0.7140 (t0) REVERT: N 349 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7989 (ttm110) REVERT: N 504 ARG cc_start: 0.8081 (OUTLIER) cc_final: 0.7452 (ttm110) REVERT: N 530 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8140 (mm110) REVERT: N 564 CYS cc_start: 0.8716 (OUTLIER) cc_final: 0.7981 (p) outliers start: 50 outliers final: 24 residues processed: 225 average time/residue: 0.8294 time to fit residues: 207.2338 Evaluate side-chains 219 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 187 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 58 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.9980 chunk 60 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 chunk 126 optimal weight: 5.9990 chunk 61 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 chunk 66 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN M 88 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.136938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.090692 restraints weight = 26811.992| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.58 r_work: 0.2890 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2742 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2742 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.0777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.185 22112 Z= 0.202 Angle : 0.616 14.131 31201 Z= 0.327 Chirality : 0.045 0.282 3459 Planarity : 0.004 0.039 3007 Dihedral : 27.357 176.817 5418 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.11 % Allowed : 22.85 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.22 (0.20), residues: 1846 helix: 1.79 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.33 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 70 TYR 0.010 0.001 TYR F 51 PHE 0.010 0.001 PHE A 67 TRP 0.007 0.001 TRP N 436 HIS 0.004 0.001 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (22105) covalent geometry : angle 0.61616 / 0.33 (31191) SS BOND : bond 0.00460 / 0.25 ( 5) SS BOND : angle 0.72366 / 0.47 ( 10) hydrogen bonds : bond 0.05536 / 3.74 ( 1046) hydrogen bonds : angle 3.61892 / 2.63 ( 2730) Misc. bond : bond 0.18132 / 12.54 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 189 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8967 (OUTLIER) cc_final: 0.8222 (mtm) REVERT: C 73 ASN cc_start: 0.7892 (t0) cc_final: 0.7448 (t160) REVERT: C 92 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.8233 (mp0) REVERT: E 42 ARG cc_start: 0.7769 (mtt-85) cc_final: 0.7460 (mmt90) REVERT: E 79 LYS cc_start: 0.8886 (tttm) cc_final: 0.8662 (tttt) REVERT: E 122 LYS cc_start: 0.8270 (ptmt) cc_final: 0.7752 (pttt) REVERT: F 93 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8013 (mm-40) REVERT: G 15 LYS cc_start: 0.8369 (mttt) cc_final: 0.7771 (mtpt) REVERT: G 95 LYS cc_start: 0.8825 (tttt) cc_final: 0.8362 (ttmt) REVERT: G 99 ARG cc_start: 0.8552 (mtp180) cc_final: 0.7848 (mmm160) REVERT: G 108 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8511 (mp) REVERT: H 28 LYS cc_start: 0.5262 (OUTLIER) cc_final: 0.5015 (tmtt) REVERT: H 68 GLU cc_start: 0.7732 (OUTLIER) cc_final: 0.7389 (tt0) REVERT: K 7 TYR cc_start: 0.8678 (m-80) cc_final: 0.8159 (m-80) REVERT: K 56 PHE cc_start: 0.8169 (m-80) cc_final: 0.7855 (m-80) REVERT: L 216 LEU cc_start: 0.7509 (mt) cc_final: 0.7112 (mp) REVERT: L 229 ARG cc_start: 0.7970 (tmm160) cc_final: 0.7665 (tmm160) REVERT: L 250 HIS cc_start: 0.8435 (OUTLIER) cc_final: 0.7871 (m90) REVERT: L 571 ASN cc_start: 0.8004 (t0) cc_final: 0.7631 (t0) REVERT: N 205 ASP cc_start: 0.7545 (t0) cc_final: 0.7124 (t0) REVERT: N 349 ARG cc_start: 0.8229 (OUTLIER) cc_final: 0.7968 (ttm110) REVERT: N 404 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: N 504 ARG cc_start: 0.8149 (OUTLIER) cc_final: 0.7475 (ttm110) REVERT: N 530 GLN cc_start: 0.8703 (OUTLIER) cc_final: 0.8147 (mm110) REVERT: N 564 CYS cc_start: 0.8723 (OUTLIER) cc_final: 0.7915 (p) outliers start: 66 outliers final: 32 residues processed: 234 average time/residue: 0.8058 time to fit residues: 209.7744 Evaluate side-chains 230 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 186 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 454 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 168 optimal weight: 8.9990 chunk 31 optimal weight: 4.9990 chunk 102 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 208 optimal weight: 5.9990 chunk 116 optimal weight: 10.0000 chunk 191 optimal weight: 1.9990 chunk 162 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN M 88 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.137692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.091570 restraints weight = 26726.959| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 1.58 r_work: 0.2905 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2758 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.0824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.188 22112 Z= 0.169 Angle : 0.594 12.471 31201 Z= 0.318 Chirality : 0.044 0.278 3459 Planarity : 0.004 0.040 3007 Dihedral : 27.333 177.363 5418 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 3.80 % Allowed : 23.04 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.31 (0.20), residues: 1846 helix: 1.86 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.28 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG M 70 TYR 0.009 0.001 TYR F 51 PHE 0.008 0.001 PHE A 67 TRP 0.008 0.001 TRP N 436 HIS 0.004 0.001 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00377 / 0.17 (22105) covalent geometry : angle 0.59356 / 0.32 (31191) SS BOND : bond 0.00296 / 0.18 ( 5) SS BOND : angle 0.73028 / 0.47 ( 10) hydrogen bonds : bond 0.05174 / 3.50 ( 1046) hydrogen bonds : angle 3.55910 / 2.59 ( 2730) Misc. bond : bond 0.18738 / 12.95 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8950 (OUTLIER) cc_final: 0.8190 (mtm) REVERT: C 73 ASN cc_start: 0.7878 (t0) cc_final: 0.7421 (t160) REVERT: E 42 ARG cc_start: 0.7774 (mtt-85) cc_final: 0.7470 (mmt90) REVERT: E 79 LYS cc_start: 0.8860 (tttm) cc_final: 0.8649 (tttt) REVERT: E 122 LYS cc_start: 0.8245 (ptmt) cc_final: 0.7729 (pttt) REVERT: G 15 LYS cc_start: 0.8357 (mttt) cc_final: 0.7768 (mtpt) REVERT: G 95 LYS cc_start: 0.8827 (tttt) cc_final: 0.8360 (ttmt) REVERT: G 99 ARG cc_start: 0.8545 (mtp180) cc_final: 0.7844 (mmm160) REVERT: G 108 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8502 (mp) REVERT: K 7 TYR cc_start: 0.8676 (m-80) cc_final: 0.8158 (m-80) REVERT: K 56 PHE cc_start: 0.8177 (m-80) cc_final: 0.7863 (m-80) REVERT: L 216 LEU cc_start: 0.7507 (mt) cc_final: 0.7105 (mp) REVERT: L 229 ARG cc_start: 0.7988 (tmm160) cc_final: 0.7672 (tmm160) REVERT: L 250 HIS cc_start: 0.8442 (OUTLIER) cc_final: 0.7859 (m90) REVERT: L 556 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7428 (t) REVERT: L 571 ASN cc_start: 0.7986 (t0) cc_final: 0.7628 (t0) REVERT: N 205 ASP cc_start: 0.7545 (t0) cc_final: 0.7127 (t0) REVERT: N 349 ARG cc_start: 0.8214 (OUTLIER) cc_final: 0.7988 (ttm110) REVERT: N 404 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: N 411 MET cc_start: 0.8112 (mtp) cc_final: 0.7757 (OUTLIER) REVERT: N 504 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7467 (ttm110) REVERT: N 530 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8134 (mm110) REVERT: N 564 CYS cc_start: 0.8717 (OUTLIER) cc_final: 0.7933 (p) outliers start: 61 outliers final: 34 residues processed: 233 average time/residue: 0.8091 time to fit residues: 209.2603 Evaluate side-chains 230 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 188 time to evaluate : 0.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 133 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 145 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 193 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 84 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 203 optimal weight: 4.9990 chunk 126 optimal weight: 0.9980 overall best weight: 2.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN M 88 GLN N 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.137450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.091288 restraints weight = 26853.933| |-----------------------------------------------------------------------------| r_work (start): 0.3072 rms_B_bonded: 1.58 r_work: 0.2899 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.0851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 22112 Z= 0.180 Angle : 0.598 12.671 31201 Z= 0.320 Chirality : 0.044 0.280 3459 Planarity : 0.004 0.039 3007 Dihedral : 27.327 177.321 5415 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.80 % Allowed : 23.23 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.29 (0.20), residues: 1846 helix: 1.83 (0.17), residues: 990 sheet: None (None), residues: 0 loop : -0.29 (0.20), residues: 856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG M 70 TYR 0.009 0.001 TYR F 51 PHE 0.009 0.001 PHE A 67 TRP 0.007 0.001 TRP N 436 HIS 0.003 0.001 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.18 (22105) covalent geometry : angle 0.59813 / 0.32 (31191) SS BOND : bond 0.00304 / 0.19 ( 5) SS BOND : angle 0.71266 / 0.46 ( 10) hydrogen bonds : bond 0.05231 / 3.53 ( 1046) hydrogen bonds : angle 3.55860 / 2.59 ( 2730) Misc. bond : bond 0.17753 / 12.26 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 191 time to evaluate : 0.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8197 (mtm) REVERT: C 73 ASN cc_start: 0.7872 (t0) cc_final: 0.7437 (t0) REVERT: D 56 MET cc_start: 0.8862 (tpp) cc_final: 0.8528 (mmm) REVERT: E 42 ARG cc_start: 0.7786 (mtt-85) cc_final: 0.7466 (mmt90) REVERT: E 79 LYS cc_start: 0.8874 (tttm) cc_final: 0.8650 (tttt) REVERT: E 122 LYS cc_start: 0.8251 (ptmt) cc_final: 0.7730 (pttt) REVERT: G 15 LYS cc_start: 0.8368 (mttt) cc_final: 0.7773 (mtpt) REVERT: G 95 LYS cc_start: 0.8830 (tttt) cc_final: 0.8347 (ttmt) REVERT: G 99 ARG cc_start: 0.8556 (mtp180) cc_final: 0.7848 (mmm160) REVERT: G 108 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8482 (mp) REVERT: H 28 LYS cc_start: 0.5253 (OUTLIER) cc_final: 0.5051 (tmtt) REVERT: H 68 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7301 (tt0) REVERT: K 7 TYR cc_start: 0.8679 (m-80) cc_final: 0.8158 (m-80) REVERT: K 56 PHE cc_start: 0.8179 (m-80) cc_final: 0.7857 (m-80) REVERT: L 216 LEU cc_start: 0.7503 (mt) cc_final: 0.7102 (mp) REVERT: L 250 HIS cc_start: 0.8427 (OUTLIER) cc_final: 0.7845 (m90) REVERT: L 556 SER cc_start: 0.7865 (OUTLIER) cc_final: 0.7431 (t) REVERT: L 571 ASN cc_start: 0.7998 (t0) cc_final: 0.7634 (t0) REVERT: M 27 ARG cc_start: 0.8480 (mtp85) cc_final: 0.7863 (mtp-110) REVERT: M 67 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7993 (mp0) REVERT: N 205 ASP cc_start: 0.7547 (t0) cc_final: 0.7131 (t0) REVERT: N 349 ARG cc_start: 0.8196 (mmp-170) cc_final: 0.7978 (ttm110) REVERT: N 404 GLU cc_start: 0.8338 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: N 411 MET cc_start: 0.8123 (mtp) cc_final: 0.7777 (OUTLIER) REVERT: N 504 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7468 (ttm110) REVERT: N 530 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8136 (mm110) REVERT: N 564 CYS cc_start: 0.8715 (OUTLIER) cc_final: 0.7922 (p) outliers start: 61 outliers final: 38 residues processed: 236 average time/residue: 0.7924 time to fit residues: 207.9304 Evaluate side-chains 236 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 188 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain D residue 29 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 28 LYS Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 399 VAL Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain L residue 556 SER Chi-restraints excluded: chain L residue 567 LEU Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 66 ASN Chi-restraints excluded: chain M residue 67 GLU Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 353 MET Chi-restraints excluded: chain N residue 400 ASP Chi-restraints excluded: chain N residue 404 GLU Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 196 optimal weight: 0.7980 chunk 153 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 82 optimal weight: 10.0000 chunk 175 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 80 GLN K 88 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.139302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.093234 restraints weight = 26716.452| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.61 r_work: 0.2930 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.197 22112 Z= 0.123 Angle : 0.574 10.765 31201 Z= 0.310 Chirality : 0.043 0.265 3459 Planarity : 0.004 0.045 3007 Dihedral : 27.271 178.188 5415 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.05 % Allowed : 24.16 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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 (0.20), residues: 1846 helix: 2.01 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.18 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE K 86 TRP 0.009 0.001 TRP N 436 HIS 0.003 0.000 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.12 (22105) covalent geometry : angle 0.57379 / 0.31 (31191) SS BOND : bond 0.00731 / 0.36 ( 5) SS BOND : angle 0.73392 / 0.46 ( 10) hydrogen bonds : bond 0.04648 / 3.15 ( 1046) hydrogen bonds : angle 3.47119 / 2.52 ( 2730) Misc. bond : bond 0.18993 / 13.09 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 195 time to evaluate : 0.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7805 (t0) cc_final: 0.7390 (t0) REVERT: C 92 GLU cc_start: 0.8455 (mm-30) cc_final: 0.8216 (mp0) REVERT: D 56 MET cc_start: 0.8812 (tpp) cc_final: 0.8511 (mmm) REVERT: E 42 ARG cc_start: 0.7759 (mtt-85) cc_final: 0.7448 (mmt90) REVERT: E 79 LYS cc_start: 0.8855 (tttm) cc_final: 0.8645 (tttt) REVERT: E 122 LYS cc_start: 0.8177 (ptmt) cc_final: 0.7661 (pttt) REVERT: G 15 LYS cc_start: 0.8319 (mttt) cc_final: 0.7741 (mtpt) REVERT: G 95 LYS cc_start: 0.8828 (tttt) cc_final: 0.8338 (ttmt) REVERT: G 99 ARG cc_start: 0.8545 (mtp180) cc_final: 0.7840 (mmm160) REVERT: G 108 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8468 (mp) REVERT: H 68 GLU cc_start: 0.7681 (OUTLIER) cc_final: 0.7244 (tt0) REVERT: K 7 TYR cc_start: 0.8651 (m-80) cc_final: 0.8129 (m-80) REVERT: K 56 PHE cc_start: 0.8159 (m-80) cc_final: 0.7828 (m-80) REVERT: L 216 LEU cc_start: 0.7506 (mt) cc_final: 0.7107 (mp) REVERT: L 250 HIS cc_start: 0.8409 (OUTLIER) cc_final: 0.7821 (m90) REVERT: L 571 ASN cc_start: 0.7973 (t0) cc_final: 0.7621 (t0) REVERT: M 27 ARG cc_start: 0.8459 (mtp85) cc_final: 0.7839 (mtp-110) REVERT: N 205 ASP cc_start: 0.7554 (t0) cc_final: 0.7133 (t0) REVERT: N 349 ARG cc_start: 0.8190 (OUTLIER) cc_final: 0.7973 (ttm110) REVERT: N 411 MET cc_start: 0.8145 (mtp) cc_final: 0.7843 (OUTLIER) REVERT: N 504 ARG cc_start: 0.8108 (OUTLIER) cc_final: 0.7446 (ttm110) REVERT: N 530 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8119 (mm110) REVERT: N 564 CYS cc_start: 0.8708 (OUTLIER) cc_final: 0.7893 (p) outliers start: 49 outliers final: 28 residues processed: 230 average time/residue: 0.8162 time to fit residues: 208.4112 Evaluate side-chains 223 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 189 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 250 HIS Chi-restraints excluded: chain L residue 253 LEU Chi-restraints excluded: chain L residue 310 LEU Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain M residue 76 LEU Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 310 LEU Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 349 ARG Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 530 GLN Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 84 optimal weight: 20.0000 chunk 6 optimal weight: 0.6980 chunk 150 optimal weight: 0.6980 chunk 192 optimal weight: 4.9990 chunk 69 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 86 optimal weight: 20.0000 chunk 147 optimal weight: 5.9990 chunk 145 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 46 HIS D 60 ASN E 125 GLN K 80 GLN ** K 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 133 ASN M 75 GLN N 140 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.095109 restraints weight = 26859.237| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 1.61 r_work: 0.2949 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2802 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.187 22112 Z= 0.122 Angle : 0.560 9.635 31201 Z= 0.305 Chirality : 0.042 0.268 3459 Planarity : 0.004 0.045 3007 Dihedral : 27.167 179.467 5414 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.43 % Allowed : 24.72 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.63 (0.20), residues: 1846 helix: 2.12 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.12 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.009 0.001 TYR H 37 PHE 0.008 0.001 PHE E 67 TRP 0.009 0.001 TRP K 89 HIS 0.002 0.000 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.12 (22105) covalent geometry : angle 0.56014 / 0.30 (31191) SS BOND : bond 0.00273 / 0.17 ( 5) SS BOND : angle 0.68991 / 0.43 ( 10) hydrogen bonds : bond 0.04400 / 2.99 ( 1046) hydrogen bonds : angle 3.39759 / 2.47 ( 2730) Misc. bond : bond 0.17691 / 12.17 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 190 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7767 (t0) cc_final: 0.7397 (t0) REVERT: C 92 GLU cc_start: 0.8460 (mm-30) cc_final: 0.8220 (mp0) REVERT: E 42 ARG cc_start: 0.7732 (mtt-85) cc_final: 0.7439 (mmt90) REVERT: E 79 LYS cc_start: 0.8828 (tttm) cc_final: 0.8602 (tttt) REVERT: E 122 LYS cc_start: 0.8154 (ptmt) cc_final: 0.7640 (pttt) REVERT: G 15 LYS cc_start: 0.8283 (mttt) cc_final: 0.7701 (mtpt) REVERT: G 95 LYS cc_start: 0.8818 (tttt) cc_final: 0.8344 (ttmt) REVERT: G 99 ARG cc_start: 0.8523 (mtp180) cc_final: 0.7824 (mmm160) REVERT: G 108 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8455 (mp) REVERT: H 68 GLU cc_start: 0.7678 (OUTLIER) cc_final: 0.7241 (tt0) REVERT: K 7 TYR cc_start: 0.8638 (m-80) cc_final: 0.8137 (m-80) REVERT: K 56 PHE cc_start: 0.8168 (m-80) cc_final: 0.7835 (m-80) REVERT: L 216 LEU cc_start: 0.7483 (mt) cc_final: 0.7075 (mp) REVERT: L 229 ARG cc_start: 0.7887 (tmm160) cc_final: 0.7670 (tmm160) REVERT: M 27 ARG cc_start: 0.8445 (mtp85) cc_final: 0.7835 (mtp-110) REVERT: N 205 ASP cc_start: 0.7552 (t0) cc_final: 0.7128 (t0) REVERT: N 349 ARG cc_start: 0.8161 (mmp-170) cc_final: 0.7941 (ttm110) REVERT: N 411 MET cc_start: 0.8167 (mtp) cc_final: 0.7957 (OUTLIER) REVERT: N 504 ARG cc_start: 0.8085 (OUTLIER) cc_final: 0.7433 (ttm110) REVERT: N 564 CYS cc_start: 0.8688 (OUTLIER) cc_final: 0.7868 (p) outliers start: 39 outliers final: 22 residues processed: 220 average time/residue: 0.7683 time to fit residues: 188.4728 Evaluate side-chains 211 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 186 time to evaluate : 0.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 22 LEU Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 202 ARG Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 149 optimal weight: 3.9990 chunk 153 optimal weight: 0.8980 chunk 42 optimal weight: 0.8980 chunk 93 optimal weight: 10.0000 chunk 111 optimal weight: 7.9990 chunk 103 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 43 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 0.9990 chunk 130 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 75 GLN K 80 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.140789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.094843 restraints weight = 26870.075| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 1.61 r_work: 0.2957 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.204 22112 Z= 0.123 Angle : 0.553 9.018 31201 Z= 0.302 Chirality : 0.041 0.270 3459 Planarity : 0.004 0.046 3007 Dihedral : 27.103 179.570 5412 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.12 % Allowed : 24.91 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.71 (0.20), residues: 1846 helix: 2.17 (0.17), residues: 989 sheet: None (None), residues: 0 loop : -0.07 (0.20), residues: 857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG M 70 TYR 0.009 0.001 TYR H 37 PHE 0.008 0.001 PHE K 86 TRP 0.008 0.001 TRP K 89 HIS 0.002 0.000 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.12 (22105) covalent geometry : angle 0.55296 / 0.30 (31191) SS BOND : bond 0.00259 / 0.16 ( 5) SS BOND : angle 0.65671 / 0.43 ( 10) hydrogen bonds : bond 0.04304 / 2.92 ( 1046) hydrogen bonds : angle 3.36822 / 2.45 ( 2730) Misc. bond : bond 0.18358 / 12.58 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3692 Ramachandran restraints generated. 1846 Oldfield, 0 Emsley, 1846 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.703 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 73 ASN cc_start: 0.7768 (t0) cc_final: 0.7427 (t0) REVERT: C 92 GLU cc_start: 0.8429 (mm-30) cc_final: 0.8183 (mp0) REVERT: D 56 MET cc_start: 0.8741 (tpp) cc_final: 0.8510 (mmm) REVERT: E 42 ARG cc_start: 0.7723 (mtt-85) cc_final: 0.7431 (mmt90) REVERT: E 79 LYS cc_start: 0.8824 (tttm) cc_final: 0.8539 (tttt) REVERT: E 122 LYS cc_start: 0.8155 (ptmt) cc_final: 0.7631 (pttt) REVERT: G 15 LYS cc_start: 0.8255 (mttt) cc_final: 0.7680 (mtpt) REVERT: G 95 LYS cc_start: 0.8819 (tttt) cc_final: 0.8341 (ttmt) REVERT: G 99 ARG cc_start: 0.8522 (mtp180) cc_final: 0.7830 (mmm160) REVERT: G 108 LEU cc_start: 0.8987 (OUTLIER) cc_final: 0.8473 (mp) REVERT: H 68 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.7263 (tt0) REVERT: K 7 TYR cc_start: 0.8645 (m-80) cc_final: 0.8156 (m-80) REVERT: K 56 PHE cc_start: 0.8169 (m-80) cc_final: 0.7842 (m-80) REVERT: L 216 LEU cc_start: 0.7492 (mt) cc_final: 0.7109 (mp) REVERT: L 229 ARG cc_start: 0.7931 (tmm160) cc_final: 0.7717 (tmm160) REVERT: M 27 ARG cc_start: 0.8445 (mtp85) cc_final: 0.7844 (mtp-110) REVERT: M 67 GLU cc_start: 0.8162 (tp30) cc_final: 0.7885 (mp0) REVERT: N 205 ASP cc_start: 0.7554 (t0) cc_final: 0.7151 (t0) REVERT: N 413 ILE cc_start: 0.8133 (pt) cc_final: 0.7793 (pp) REVERT: N 504 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7445 (ttp-170) outliers start: 34 outliers final: 26 residues processed: 219 average time/residue: 0.7033 time to fit residues: 171.8644 Evaluate side-chains 220 residues out of total 1606 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 191 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain H residue 54 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 9 THR Chi-restraints excluded: chain K residue 97 LEU Chi-restraints excluded: chain L residue 171 VAL Chi-restraints excluded: chain L residue 219 ASP Chi-restraints excluded: chain L residue 395 ASN Chi-restraints excluded: chain L residue 470 THR Chi-restraints excluded: chain L residue 541 THR Chi-restraints excluded: chain M residue 52 LYS Chi-restraints excluded: chain N residue 176 VAL Chi-restraints excluded: chain N residue 330 ASN Chi-restraints excluded: chain N residue 411 MET Chi-restraints excluded: chain N residue 447 THR Chi-restraints excluded: chain N residue 478 MET Chi-restraints excluded: chain N residue 504 ARG Chi-restraints excluded: chain N residue 564 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 209 random chunks: chunk 29 optimal weight: 0.5980 chunk 153 optimal weight: 0.7980 chunk 112 optimal weight: 0.0980 chunk 70 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 76 optimal weight: 10.0000 chunk 180 optimal weight: 1.9990 chunk 169 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 72 optimal weight: 20.0000 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 60 ASN E 125 GLN K 66 ASN ** K 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 80 GLN K 88 GLN L 133 ASN M 75 GLN N 133 ASN N 140 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.141935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.095714 restraints weight = 26891.323| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.61 r_work: 0.2965 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.197 22112 Z= 0.117 Angle : 0.555 8.659 31201 Z= 0.303 Chirality : 0.041 0.267 3459 Planarity : 0.004 0.089 3007 Dihedral : 27.089 179.480 5410 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.12 % Allowed : 25.03 % Favored : 72.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.36 % 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: 1.76 (0.20), residues: 1846 helix: 2.20 (0.17), residues: 991 sheet: None (None), residues: 0 loop : -0.05 (0.20), residues: 855 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG N 349 TYR 0.009 0.001 TYR H 37 PHE 0.008 0.001 PHE K 86 TRP 0.008 0.001 TRP K 89 HIS 0.002 0.000 HIS L 257 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.12 (22105) covalent geometry : angle 0.55462 / 0.30 (31191) SS BOND : bond 0.00271 / 0.16 ( 5) SS BOND : angle 0.63472 / 0.41 ( 10) hydrogen bonds : bond 0.04216 / 2.86 ( 1046) hydrogen bonds : angle 3.35755 / 2.45 ( 2730) Misc. bond : bond 0.18019 / 12.36 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7007.02 seconds wall clock time: 119 minutes 52.87 seconds (7192.87 seconds total)