Starting phenix.real_space_refine on Sat Aug 23 18:06:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcb_37098/08_2025/8kcb_37098.map" } resolution = 3.17 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= 0.004 sd= 0.036 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: 7 Type Number sf(0) Gaussians P 253 5.49 5 S 23 5.16 5 Be 1 3.05 5 C 8111 2.51 5 N 2580 2.21 5 O 3100 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 14071 Number of models: 1 Model: "" Number of chains: 12 Chain: "D" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 666 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 83} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 672 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 24 Planarities with less than four sites: {'TYR:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 726 Classifications: {'peptide': 90} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 87} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 691 Classifications: {'peptide': 89} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 2, 'TRANS': 86} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 40 Unresolved non-hydrogen dihedrals: 28 Planarities with less than four sites: {'ARG:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 27 Chain: "H" Number of atoms: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 704 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 86} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "G" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 615 Classifications: {'peptide': 77} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 75} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "A" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 662 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "B" Number of atoms: 613 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 613 Classifications: {'peptide': 89} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PTRANS': 3, 'TRANS': 85} Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 74 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 4, 'GLU:plan': 3, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 41 Chain: "I" Number of atoms: 2563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2563 Classifications: {'DNA': 126} Link IDs: {'rna3p': 125} Chain: "J" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 2600 Classifications: {'DNA': 126} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 125} Chain: "K" Number of atoms: 3528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 486, 3528 Classifications: {'peptide': 486} Incomplete info: {'truncation_to_alanine': 110} Link IDs: {'PTRANS': 20, 'TRANS': 465} Chain breaks: 4 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 448 Unresolved non-hydrogen angles: 559 Unresolved non-hydrogen dihedrals: 378 Unresolved non-hydrogen chiralities: 22 Planarities with less than four sites: {'GLU:plan': 12, 'GLN:plan1': 11, 'ASN:plan1': 4, 'HIS:plan': 5, 'ASP:plan': 15, 'PHE:plan': 7, 'TRP:plan': 1, 'ARG:plan': 8, 'TYR:plan': 3} Unresolved non-hydrogen planarities: 286 Chain: "K" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Unusual residues: {'ADP': 1, 'BEF': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 3.42, per 1000 atoms: 0.24 Number of scatterers: 14071 At special positions: 0 Unit cell: (137.78, 100.43, 138.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 23 16.00 P 253 15.00 F 3 9.00 O 3100 8.00 N 2580 7.00 C 8111 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.15 Conformation dependent library (CDL) restraints added in 408.4 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2224 Finding SS restraints... Secondary structure from input PDB file: 57 helices and 10 sheets defined 69.1% alpha, 5.5% beta 36 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'D' and resid 57 through 69 Processing helix chain 'D' and resid 75 through 104 Processing helix chain 'D' and resid 110 through 122 Processing helix chain 'D' and resid 123 through 142 removed outlier: 3.840A pdb=" N HIS D 129 " --> pdb=" O GLU D 125 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER D 132 " --> pdb=" O LYS D 128 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 69 Processing helix chain 'C' and resid 75 through 104 Processing helix chain 'C' and resid 110 through 122 removed outlier: 3.525A pdb=" N ILE C 114 " --> pdb=" O THR C 110 " (cutoff:3.500A) Processing helix chain 'C' and resid 124 through 143 removed outlier: 3.975A pdb=" N LYS C 128 " --> pdb=" O GLY C 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 47 through 57 Processing helix chain 'F' and resid 63 through 79 removed outlier: 3.598A pdb=" N PHE F 67 " --> pdb=" O ARG F 63 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N ASP F 77 " --> pdb=" O GLU F 73 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N PHE F 78 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 114 Processing helix chain 'F' and resid 120 through 132 Processing helix chain 'E' and resid 48 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.609A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.544A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 29 removed outlier: 3.686A pdb=" N ILE H 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 30 through 42 Processing helix chain 'H' and resid 49 through 76 removed outlier: 3.530A pdb=" N ALA H 76 " --> pdb=" O TYR H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 94 removed outlier: 3.508A pdb=" N VAL H 86 " --> pdb=" O THR H 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 25 through 29 removed outlier: 3.580A pdb=" N ILE G 29 " --> pdb=" O ILE G 26 " (cutoff:3.500A) Processing helix chain 'G' and resid 30 through 42 Processing helix chain 'G' and resid 48 through 76 removed outlier: 4.368A pdb=" N GLU G 52 " --> pdb=" O GLY G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL G 86 " --> pdb=" O THR G 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 18 through 23 removed outlier: 3.571A pdb=" N ALA A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 38 Processing helix chain 'A' and resid 46 through 74 removed outlier: 4.368A pdb=" N VAL A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 91 removed outlier: 3.740A pdb=" N ARG A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ASN A 90 " --> pdb=" O LEU A 86 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ASP A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 98 Processing helix chain 'B' and resid 18 through 23 Processing helix chain 'B' and resid 27 through 38 removed outlier: 3.567A pdb=" N ILE B 31 " --> pdb=" O PRO B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 46 through 74 removed outlier: 4.315A pdb=" N VAL B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 91 removed outlier: 3.512A pdb=" N ILE B 84 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 99 Processing helix chain 'K' and resid 185 through 194 removed outlier: 3.678A pdb=" N ASN K 191 " --> pdb=" O ILE K 187 " (cutoff:3.500A) Processing helix chain 'K' and resid 203 through 220 Processing helix chain 'K' and resid 233 through 247 removed outlier: 3.538A pdb=" N ASN K 247 " --> pdb=" O HIS K 243 " (cutoff:3.500A) Processing helix chain 'K' and resid 258 through 273 removed outlier: 4.350A pdb=" N SER K 263 " --> pdb=" O LEU K 259 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ASN K 264 " --> pdb=" O SER K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 284 through 296 Processing helix chain 'K' and resid 310 through 318 Processing helix chain 'K' and resid 335 through 339 Processing helix chain 'K' and resid 343 through 352 removed outlier: 3.532A pdb=" N ARG K 347 " --> pdb=" O CYS K 343 " (cutoff:3.500A) Processing helix chain 'K' and resid 369 through 380 Processing helix chain 'K' and resid 386 through 394 removed outlier: 3.642A pdb=" N PHE K 390 " --> pdb=" O SER K 386 " (cutoff:3.500A) Processing helix chain 'K' and resid 411 through 425 removed outlier: 3.535A pdb=" N GLY K 422 " --> pdb=" O SER K 418 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE K 423 " --> pdb=" O LYS K 419 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N LEU K 424 " --> pdb=" O LEU K 420 " (cutoff:3.500A) Processing helix chain 'K' and resid 432 through 437 removed outlier: 3.502A pdb=" N VAL K 436 " --> pdb=" O MET K 432 " (cutoff:3.500A) Processing helix chain 'K' and resid 453 through 463 Processing helix chain 'K' and resid 490 through 498 Processing helix chain 'K' and resid 499 through 509 removed outlier: 4.353A pdb=" N LEU K 503 " --> pdb=" O HIS K 499 " (cutoff:3.500A) Processing helix chain 'K' and resid 515 through 523 Processing helix chain 'K' and resid 525 through 540 Processing helix chain 'K' and resid 549 through 564 Processing helix chain 'K' and resid 575 through 588 Processing helix chain 'K' and resid 623 through 633 removed outlier: 3.733A pdb=" N ASP K 627 " --> pdb=" O ASN K 623 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 672 removed outlier: 3.962A pdb=" N ARG K 657 " --> pdb=" O SER K 653 " (cutoff:3.500A) Processing helix chain 'K' and resid 706 through 711 Processing helix chain 'K' and resid 714 through 723 Processing sheet with id=AA1, first strand: chain 'D' and resid 73 through 74 removed outlier: 7.551A pdb=" N GLY D 73 " --> pdb=" O ILE A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 108 through 109 Processing sheet with id=AA3, first strand: chain 'C' and resid 73 through 74 removed outlier: 7.392A pdb=" N GLY C 73 " --> pdb=" O ILE B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 108 through 109 Processing sheet with id=AA5, first strand: chain 'F' and resid 83 through 84 removed outlier: 6.927A pdb=" N ARG F 83 " --> pdb=" O VAL H 81 " (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: 6.875A pdb=" N ARG E 83 " --> pdb=" O VAL G 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'H' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'G' and resid 96 through 97 removed outlier: 6.521A pdb=" N THR G 96 " --> pdb=" O THR B 102 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 278 through 279 removed outlier: 6.864A pdb=" N TYR K 253 " --> pdb=" O VAL K 307 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N THR K 309 " --> pdb=" O TYR K 253 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N VAL K 255 " --> pdb=" O THR K 309 " (cutoff:3.500A) removed outlier: 7.519A pdb=" N LYS K 328 " --> pdb=" O MET K 354 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N ILE K 224 " --> pdb=" O LEU K 429 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 567 through 570 removed outlier: 6.272A pdb=" N CYS K 568 " --> pdb=" O LEU K 597 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N SER K 599 " --> pdb=" O CYS K 568 " (cutoff:3.500A) removed outlier: 7.920A pdb=" N ILE K 570 " --> pdb=" O SER K 599 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N VAL K 543 " --> pdb=" O PHE K 596 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N LEU K 598 " --> pdb=" O VAL K 543 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE K 545 " --> pdb=" O LEU K 598 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LEU K 544 " --> pdb=" O ILE K 616 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALA K 450 " --> pdb=" O SER K 649 " (cutoff:3.500A) 582 hydrogen bonds defined for protein. 1728 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 81 hydrogen bonds 134 hydrogen bond angles 0 basepair planarities 36 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 2.63 Time building geometry restraints manager: 1.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2963 1.33 - 1.45: 4228 1.45 - 1.57: 7096 1.57 - 1.69: 505 1.69 - 1.81: 38 Bond restraints: 14830 Sorted by residual: bond pdb=" F2 BEF K 901 " pdb="BE BEF K 901 " ideal model delta sigma weight residual 1.476 1.710 -0.234 2.00e-02 2.50e+03 1.37e+02 bond pdb=" F1 BEF K 901 " pdb="BE BEF K 901 " ideal model delta sigma weight residual 1.476 1.706 -0.230 2.00e-02 2.50e+03 1.32e+02 bond pdb=" F3 BEF K 901 " pdb="BE BEF K 901 " ideal model delta sigma weight residual 1.476 1.690 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" C4 ADP K 902 " pdb=" C5 ADP K 902 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" C5 ADP K 902 " pdb=" C6 ADP K 902 " ideal model delta sigma weight residual 1.490 1.407 0.083 2.00e-02 2.50e+03 1.73e+01 ... (remaining 14825 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.09: 21132 4.09 - 8.18: 29 8.18 - 12.27: 5 12.27 - 16.36: 1 16.36 - 20.45: 1 Bond angle restraints: 21168 Sorted by residual: angle pdb=" F1 BEF K 901 " pdb="BE BEF K 901 " pdb=" F3 BEF K 901 " ideal model delta sigma weight residual 120.12 99.67 20.45 3.00e+00 1.11e-01 4.65e+01 angle pdb=" F2 BEF K 901 " pdb="BE BEF K 901 " pdb=" F3 BEF K 901 " ideal model delta sigma weight residual 119.96 104.61 15.35 3.00e+00 1.11e-01 2.62e+01 angle pdb=" C4' DG J 4 " pdb=" C3' DG J 4 " pdb=" O3' DG J 4 " ideal model delta sigma weight residual 110.00 117.05 -7.05 1.50e+00 4.44e-01 2.21e+01 angle pdb=" N LYS H 20 " pdb=" CA LYS H 20 " pdb=" C LYS H 20 " ideal model delta sigma weight residual 111.39 105.04 6.35 1.38e+00 5.25e-01 2.12e+01 angle pdb=" C4' DC I 2 " pdb=" C3' DC I 2 " pdb=" O3' DC I 2 " ideal model delta sigma weight residual 110.00 116.29 -6.29 1.50e+00 4.44e-01 1.76e+01 ... (remaining 21163 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.99: 7034 35.99 - 71.98: 1117 71.98 - 107.97: 53 107.97 - 143.96: 7 143.96 - 179.95: 4 Dihedral angle restraints: 8215 sinusoidal: 4787 harmonic: 3428 Sorted by residual: dihedral pdb=" C4' ADP K 902 " pdb=" C5' ADP K 902 " pdb=" O5' ADP K 902 " pdb=" PA ADP K 902 " ideal model delta sinusoidal sigma weight residual 180.00 58.48 121.52 1 2.00e+01 2.50e-03 3.65e+01 dihedral pdb=" C4' DC J 122 " pdb=" C3' DC J 122 " pdb=" O3' DC J 122 " pdb=" P DC J 123 " ideal model delta sinusoidal sigma weight residual -140.00 39.95 -179.95 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 45 " pdb=" C3' DT J 45 " pdb=" O3' DT J 45 " pdb=" P DT J 46 " ideal model delta sinusoidal sigma weight residual 220.00 41.44 178.56 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 8212 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 2241 0.056 - 0.112: 207 0.112 - 0.168: 15 0.168 - 0.224: 0 0.224 - 0.280: 3 Chirality restraints: 2466 Sorted by residual: chirality pdb=" C3' DC I 2 " pdb=" C4' DC I 2 " pdb=" O3' DC I 2 " pdb=" C2' DC I 2 " both_signs ideal model delta sigma weight residual False -2.66 -2.38 -0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" C3' DC J 122 " pdb=" C4' DC J 122 " pdb=" O3' DC J 122 " pdb=" C2' DC J 122 " both_signs ideal model delta sigma weight residual False -2.66 -2.40 -0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" C3' DC I 1 " pdb=" C4' DC I 1 " pdb=" O3' DC I 1 " pdb=" C2' DC I 1 " both_signs ideal model delta sigma weight residual False -2.66 -2.43 -0.23 2.00e-01 2.50e+01 1.35e+00 ... (remaining 2463 not shown) Planarity restraints: 1798 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I 21 " 0.020 2.00e-02 2.50e+03 9.46e-03 2.46e+00 pdb=" N9 DA I 21 " -0.023 2.00e-02 2.50e+03 pdb=" C8 DA I 21 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 21 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 21 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 21 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I 21 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA I 21 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 21 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I 21 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I 21 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 97 " 0.019 2.00e-02 2.50e+03 8.74e-03 2.10e+00 pdb=" N9 DA I 97 " -0.021 2.00e-02 2.50e+03 pdb=" C8 DA I 97 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I 97 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 97 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DA I 97 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 97 " 0.003 2.00e-02 2.50e+03 pdb=" N1 DA I 97 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 97 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 97 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 97 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 82 " -0.018 2.00e-02 2.50e+03 8.23e-03 1.86e+00 pdb=" N9 DA I 82 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA I 82 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 82 " -0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 82 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I 82 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I 82 " -0.005 2.00e-02 2.50e+03 pdb=" N1 DA I 82 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 82 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 82 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 82 " 0.002 2.00e-02 2.50e+03 ... (remaining 1795 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 3736 2.82 - 3.34: 13390 3.34 - 3.86: 25672 3.86 - 4.38: 28813 4.38 - 4.90: 43270 Nonbonded interactions: 114881 Sorted by model distance: nonbonded pdb=" OE1 GLN K 206 " pdb=" N6 ADP K 902 " model vdw 2.302 3.120 nonbonded pdb=" O2 DT I 48 " pdb=" N2 DG J 80 " model vdw 2.307 3.120 nonbonded pdb=" NE2 HIS K 336 " pdb=" OG1 THR K 363 " model vdw 2.329 3.120 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.338 3.120 nonbonded pdb=" O ILE E 119 " pdb=" OG SER G 47 " model vdw 2.338 3.040 ... (remaining 114876 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 17 or (resid 18 and (name N or name CA or name C or name O \ or name CB )) or resid 19 through 20 or (resid 21 through 22 and (name N or nam \ e CA or name C or name O or name CB )) or resid 23 through 32 or (resid 33 and ( \ name N or name CA or name C or name O or name CB )) or resid 34 through 71 or (r \ esid 72 and (name N or name CA or name C or name O or name CB )) or resid 73 thr \ ough 74 or (resid 75 through 76 and (name N or name CA or name C or name O or na \ me CB )) or resid 77 through 89 or (resid 90 through 93 and (name N or name CA o \ r name C or name O or name CB )) or resid 94 through 95 or (resid 96 and (name N \ or name CA or name C or name O or name CB )) or resid 97 through 99 or (resid 1 \ 00 through 101 and (name N or name CA or name C or name O or name CB )) or resid \ 102 through 105)) selection = chain 'B' } ncs_group { reference = (chain 'C' and (resid 56 through 103 or (resid 104 through 105 and (name N or na \ me CA or name C or name O or name CB )) or resid 106 through 142)) selection = (chain 'D' and (resid 56 through 57 or (resid 58 and (name N or name CA or name \ C or name O or name CB )) or resid 59 through 62 or (resid 63 and (name N or nam \ e CA or name C or name O or name CB )) or resid 64 through 65 or (resid 66 and ( \ name N or name CA or name C or name O or name CB )) or resid 67 through 76 or (r \ esid 77 through 78 and (name N or name CA or name C or name O or name CB )) or r \ esid 79 through 142)) } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 47 through 48 or (resid 49 through 50 and (name N or name \ CA or name C or name O or name CB )) or resid 51 or (resid 52 and (name N or nam \ e CA or name C or name O or name CB )) or resid 53 through 78 or (resid 79 and ( \ name N or name CA or name C or name O or name CB )) or resid 80 through 93 or (r \ esid 94 through 96 and (name N or name CA or name C or name O or name CB )) or r \ esid 97 through 132 or (resid 133 through 134 and (name N or name CA or name C o \ r name O or name CB )) or resid 135)) } ncs_group { reference = chain 'G' selection = (chain 'H' and (resid 24 through 76 or (resid 77 and (name N or name CA or name \ C or name O or name CB )) or resid 78 through 100)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.850 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: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.650 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.310 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7634 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.234 14830 Z= 0.226 Angle : 0.571 20.450 21168 Z= 0.326 Chirality : 0.033 0.280 2466 Planarity : 0.003 0.027 1798 Dihedral : 26.342 179.954 5991 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.62 % Rotamer: Outliers : 0.23 % Allowed : 1.84 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.21), residues: 1158 helix: -0.29 (0.16), residues: 760 sheet: -0.60 (0.60), residues: 60 loop : -1.91 (0.27), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 92 TYR 0.020 0.001 TYR G 72 PHE 0.005 0.001 PHE C 90 TRP 0.004 0.000 TRP K 373 HIS 0.004 0.001 HIS H 18 Details of bonding type rmsd covalent geometry : bond 0.00452 (14830) covalent geometry : angle 0.57057 (21168) hydrogen bonds : bond 0.18793 ( 663) hydrogen bonds : angle 6.52089 ( 1862) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 291 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 71 ASP cc_start: 0.8485 (p0) cc_final: 0.8127 (p0) REVERT: C 88 ASP cc_start: 0.9011 (t0) cc_final: 0.8634 (t0) REVERT: C 91 GLU cc_start: 0.8751 (tm-30) cc_final: 0.8415 (tm-30) REVERT: F 73 GLU cc_start: 0.8326 (tt0) cc_final: 0.8032 (tt0) REVERT: E 60 LEU cc_start: 0.8840 (mt) cc_final: 0.8223 (mm) REVERT: E 97 GLU cc_start: 0.8415 (tt0) cc_final: 0.8032 (tt0) REVERT: E 118 THR cc_start: 0.9113 (m) cc_final: 0.8762 (p) REVERT: H 91 LYS cc_start: 0.9183 (tttt) cc_final: 0.8821 (tttm) REVERT: G 79 LYS cc_start: 0.8649 (mmtt) cc_final: 0.8213 (mmmm) REVERT: A 33 ARG cc_start: 0.9147 (ttp-170) cc_final: 0.8766 (ttp80) REVERT: A 62 GLU cc_start: 0.8752 (tp30) cc_final: 0.8513 (tp30) REVERT: B 65 GLU cc_start: 0.8724 (tt0) cc_final: 0.8319 (tm-30) REVERT: B 73 ASP cc_start: 0.8927 (m-30) cc_final: 0.8638 (m-30) REVERT: K 315 MET cc_start: 0.9135 (ttp) cc_final: 0.8848 (ttt) REVERT: K 571 ASP cc_start: 0.7754 (t0) cc_final: 0.7337 (t0) outliers start: 2 outliers final: 0 residues processed: 293 average time/residue: 0.1745 time to fit residues: 67.2749 Evaluate side-chains 182 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 182 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 10.0000 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 20.0000 chunk 55 optimal weight: 10.0000 overall best weight: 5.7390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 69 HIS C 83 ASN C 87 ASN F 125 GLN E 68 GLN E 125 GLN G 64 ASN A 85 GLN B 74 ASN K 219 ASN K 351 HIS K 421 HIS K 456 GLN K 498 ASN K 548 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3849 r_free = 0.3849 target = 0.084602 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3169 r_free = 0.3169 target = 0.055420 restraints weight = 56121.739| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 3.23 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.063 14830 Z= 0.366 Angle : 0.719 7.340 21168 Z= 0.402 Chirality : 0.042 0.189 2466 Planarity : 0.005 0.047 1798 Dihedral : 31.056 177.633 4014 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.47 % Favored : 98.45 % Rotamer: Outliers : 3.57 % Allowed : 14.27 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.23), residues: 1158 helix: 1.60 (0.18), residues: 763 sheet: -0.21 (0.55), residues: 69 loop : -1.58 (0.29), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG H 19 TYR 0.015 0.002 TYR E 54 PHE 0.012 0.002 PHE D 62 TRP 0.009 0.002 TRP K 212 HIS 0.009 0.002 HIS C 69 Details of bonding type rmsd covalent geometry : bond 0.00815 (14830) covalent geometry : angle 0.71908 (21168) hydrogen bonds : bond 0.06959 ( 663) hydrogen bonds : angle 4.15517 ( 1862) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 174 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8899 (t0) cc_final: 0.8570 (t0) REVERT: D 113 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8368 (mp0) REVERT: C 71 ASP cc_start: 0.8897 (p0) cc_final: 0.8637 (p0) REVERT: C 88 ASP cc_start: 0.9172 (t0) cc_final: 0.8729 (t0) REVERT: C 91 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8623 (tm-30) REVERT: C 125 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8146 (tp30) REVERT: C 133 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8936 (tp30) REVERT: F 53 LYS cc_start: 0.8598 (tttt) cc_final: 0.8392 (tppt) REVERT: F 55 GLN cc_start: 0.7953 (mt0) cc_final: 0.7571 (mt0) REVERT: F 56 LYS cc_start: 0.8555 (tttt) cc_final: 0.8285 (mtpt) REVERT: E 60 LEU cc_start: 0.8930 (mt) cc_final: 0.8639 (mt) REVERT: E 97 GLU cc_start: 0.8103 (tt0) cc_final: 0.7746 (tt0) REVERT: H 27 GLN cc_start: 0.8445 (tm-30) cc_final: 0.8196 (tm-30) REVERT: H 91 LYS cc_start: 0.9236 (tttt) cc_final: 0.8767 (ttpt) REVERT: A 85 GLN cc_start: 0.9136 (tt0) cc_final: 0.8872 (tt0) REVERT: B 62 GLU cc_start: 0.8721 (tt0) cc_final: 0.8484 (tt0) REVERT: B 65 GLU cc_start: 0.8614 (tt0) cc_final: 0.8240 (tm-30) REVERT: K 315 MET cc_start: 0.9116 (ttp) cc_final: 0.8864 (ttt) REVERT: K 571 ASP cc_start: 0.8035 (t0) cc_final: 0.7753 (t0) outliers start: 31 outliers final: 16 residues processed: 195 average time/residue: 0.1317 time to fit residues: 36.4842 Evaluate side-chains 169 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 151 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain C residue 68 VAL Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain C residue 125 GLU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 548 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 83 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 6.9990 chunk 8 optimal weight: 4.9990 chunk 1 optimal weight: 7.9990 chunk 108 optimal weight: 7.9990 chunk 130 optimal weight: 30.0000 chunk 129 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 129 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.080841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.052261 restraints weight = 57353.437| |-----------------------------------------------------------------------------| r_work (start): 0.3016 rms_B_bonded: 3.24 r_work: 0.2815 rms_B_bonded: 4.98 restraints_weight: 0.5000 r_work (final): 0.2815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.5609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.071 14830 Z= 0.361 Angle : 0.688 8.064 21168 Z= 0.387 Chirality : 0.040 0.221 2466 Planarity : 0.005 0.052 1798 Dihedral : 31.164 179.486 4014 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer: Outliers : 4.26 % Allowed : 15.54 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.24), residues: 1158 helix: 2.13 (0.18), residues: 765 sheet: -0.22 (0.57), residues: 69 loop : -1.31 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 89 TYR 0.018 0.002 TYR K 311 PHE 0.014 0.002 PHE K 546 TRP 0.012 0.002 TRP K 373 HIS 0.005 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00816 (14830) covalent geometry : angle 0.68816 (21168) hydrogen bonds : bond 0.06488 ( 663) hydrogen bonds : angle 4.11290 ( 1862) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 156 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9217 (t0) cc_final: 0.8947 (t0) REVERT: D 96 GLU cc_start: 0.8864 (mm-30) cc_final: 0.8554 (mm-30) REVERT: D 113 GLU cc_start: 0.9030 (OUTLIER) cc_final: 0.8697 (mp0) REVERT: C 88 ASP cc_start: 0.9339 (t70) cc_final: 0.8851 (t0) REVERT: C 91 GLU cc_start: 0.9243 (tm-30) cc_final: 0.8940 (tm-30) REVERT: C 96 GLU cc_start: 0.8904 (mm-30) cc_final: 0.8495 (mm-30) REVERT: C 125 GLU cc_start: 0.8810 (mm-30) cc_final: 0.8309 (tp30) REVERT: F 53 LYS cc_start: 0.8656 (tttt) cc_final: 0.8407 (tppt) REVERT: F 55 GLN cc_start: 0.8014 (mt0) cc_final: 0.7667 (mt0) REVERT: F 56 LYS cc_start: 0.8629 (tttt) cc_final: 0.8305 (mtpt) REVERT: E 60 LEU cc_start: 0.8965 (mt) cc_final: 0.8409 (mt) REVERT: E 97 GLU cc_start: 0.8740 (tt0) cc_final: 0.8229 (tt0) REVERT: H 27 GLN cc_start: 0.8850 (tm-30) cc_final: 0.8492 (tm-30) REVERT: H 91 LYS cc_start: 0.9184 (tttt) cc_final: 0.8883 (ttpt) REVERT: A 59 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8968 (mp) REVERT: A 76 LYS cc_start: 0.7803 (mmtt) cc_final: 0.7362 (mttt) REVERT: A 92 GLU cc_start: 0.9139 (tp30) cc_final: 0.8845 (tp30) REVERT: A 96 LYS cc_start: 0.8909 (mttt) cc_final: 0.8505 (mttt) REVERT: B 65 GLU cc_start: 0.8885 (tt0) cc_final: 0.8490 (tm-30) REVERT: K 605 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8154 (pp) outliers start: 37 outliers final: 23 residues processed: 183 average time/residue: 0.1296 time to fit residues: 33.3261 Evaluate side-chains 168 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 87 ASN Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 74 ILE Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 548 GLN Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 637 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 86 optimal weight: 8.9990 chunk 83 optimal weight: 5.9990 chunk 131 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 134 optimal weight: 40.0000 chunk 33 optimal weight: 30.0000 chunk 126 optimal weight: 6.9990 chunk 114 optimal weight: 20.0000 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 75 HIS A 85 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.080280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.051791 restraints weight = 57231.681| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.07 r_work: 0.2838 rms_B_bonded: 4.77 restraints_weight: 0.5000 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 14830 Z= 0.271 Angle : 0.619 8.060 21168 Z= 0.350 Chirality : 0.037 0.188 2466 Planarity : 0.004 0.054 1798 Dihedral : 31.099 178.203 4014 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.81 % Favored : 98.10 % Rotamer: Outliers : 3.68 % Allowed : 18.30 % Favored : 78.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.93 (0.24), residues: 1158 helix: 2.42 (0.18), residues: 770 sheet: -0.26 (0.56), residues: 69 loop : -1.33 (0.30), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 89 TYR 0.011 0.002 TYR B 51 PHE 0.013 0.001 PHE C 62 TRP 0.013 0.001 TRP K 549 HIS 0.006 0.001 HIS G 75 Details of bonding type rmsd covalent geometry : bond 0.00613 (14830) covalent geometry : angle 0.61915 (21168) hydrogen bonds : bond 0.05670 ( 663) hydrogen bonds : angle 3.81779 ( 1862) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 159 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9081 (t0) cc_final: 0.8749 (t0) REVERT: D 113 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8640 (mp0) REVERT: C 88 ASP cc_start: 0.9261 (t70) cc_final: 0.8781 (t0) REVERT: C 91 GLU cc_start: 0.9235 (tm-30) cc_final: 0.8930 (tm-30) REVERT: C 96 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8483 (mm-30) REVERT: C 113 GLU cc_start: 0.9303 (mp0) cc_final: 0.9004 (mp0) REVERT: C 125 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8379 (tp30) REVERT: F 53 LYS cc_start: 0.8688 (tttt) cc_final: 0.8289 (tppt) REVERT: F 56 LYS cc_start: 0.8633 (tttt) cc_final: 0.8392 (mtpt) REVERT: F 62 ILE cc_start: 0.9460 (mt) cc_final: 0.9229 (mt) REVERT: E 60 LEU cc_start: 0.8860 (mt) cc_final: 0.8424 (mt) REVERT: E 97 GLU cc_start: 0.8736 (tt0) cc_final: 0.8324 (tt0) REVERT: H 27 GLN cc_start: 0.8948 (tm-30) cc_final: 0.8563 (tm-30) REVERT: H 91 LYS cc_start: 0.9201 (tttt) cc_final: 0.8814 (ttpt) REVERT: A 59 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8882 (mp) REVERT: A 89 ARG cc_start: 0.8972 (mmt90) cc_final: 0.8723 (mtm180) REVERT: A 92 GLU cc_start: 0.9033 (tp30) cc_final: 0.8823 (tp30) REVERT: A 96 LYS cc_start: 0.8917 (mttt) cc_final: 0.8646 (mttt) REVERT: B 62 GLU cc_start: 0.9030 (tt0) cc_final: 0.8812 (tt0) REVERT: B 65 GLU cc_start: 0.8924 (tt0) cc_final: 0.8566 (tm-30) REVERT: K 229 MET cc_start: 0.8360 (mpp) cc_final: 0.7424 (mtt) REVERT: K 605 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8271 (pp) outliers start: 32 outliers final: 24 residues processed: 183 average time/residue: 0.1233 time to fit residues: 32.4626 Evaluate side-chains 176 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 149 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 39 LYS Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 605 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 chunk 72 optimal weight: 4.9990 chunk 96 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 101 optimal weight: 8.9990 chunk 48 optimal weight: 3.9990 chunk 135 optimal weight: 3.9990 chunk 127 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.080194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.051947 restraints weight = 56198.583| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.05 r_work: 0.2843 rms_B_bonded: 4.76 restraints_weight: 0.5000 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.6219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14830 Z= 0.249 Angle : 0.612 6.787 21168 Z= 0.346 Chirality : 0.036 0.169 2466 Planarity : 0.004 0.055 1798 Dihedral : 31.047 177.504 4014 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.99 % Favored : 97.93 % Rotamer: Outliers : 4.49 % Allowed : 19.33 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.14 (0.24), residues: 1158 helix: 2.59 (0.18), residues: 771 sheet: -0.14 (0.56), residues: 69 loop : -1.31 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 63 TYR 0.011 0.001 TYR D 57 PHE 0.008 0.001 PHE D 141 TRP 0.009 0.001 TRP K 373 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00562 (14830) covalent geometry : angle 0.61219 (21168) hydrogen bonds : bond 0.05592 ( 663) hydrogen bonds : angle 3.74887 ( 1862) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 162 time to evaluate : 0.288 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9067 (t0) cc_final: 0.8730 (t0) REVERT: D 96 GLU cc_start: 0.8803 (mm-30) cc_final: 0.8451 (mm-30) REVERT: D 113 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: D 128 LYS cc_start: 0.9160 (mmmt) cc_final: 0.8915 (mttt) REVERT: C 88 ASP cc_start: 0.9233 (t70) cc_final: 0.8744 (t0) REVERT: C 91 GLU cc_start: 0.9212 (tm-30) cc_final: 0.8928 (tm-30) REVERT: C 113 GLU cc_start: 0.9255 (mp0) cc_final: 0.9045 (mp0) REVERT: C 125 GLU cc_start: 0.8691 (mm-30) cc_final: 0.8388 (tp30) REVERT: F 53 LYS cc_start: 0.8695 (tttt) cc_final: 0.8409 (tppt) REVERT: F 55 GLN cc_start: 0.8143 (mt0) cc_final: 0.7619 (mp10) REVERT: F 56 LYS cc_start: 0.8572 (tttt) cc_final: 0.8315 (mtpt) REVERT: E 57 SER cc_start: 0.7364 (t) cc_final: 0.7123 (t) REVERT: E 60 LEU cc_start: 0.8624 (mt) cc_final: 0.8272 (mt) REVERT: H 27 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8561 (tm-30) REVERT: H 91 LYS cc_start: 0.9168 (tttt) cc_final: 0.8814 (ttpt) REVERT: A 59 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8953 (mp) REVERT: A 76 LYS cc_start: 0.8015 (mmtt) cc_final: 0.7599 (mtmt) REVERT: A 96 LYS cc_start: 0.8980 (mttt) cc_final: 0.8717 (mttt) REVERT: B 65 GLU cc_start: 0.8930 (tt0) cc_final: 0.8575 (tm-30) REVERT: K 229 MET cc_start: 0.8307 (mpp) cc_final: 0.7443 (mtt) REVERT: K 432 MET cc_start: 0.9116 (mmm) cc_final: 0.8381 (tpp) REVERT: K 605 LEU cc_start: 0.8489 (OUTLIER) cc_final: 0.8259 (pp) outliers start: 39 outliers final: 29 residues processed: 190 average time/residue: 0.1292 time to fit residues: 34.6017 Evaluate side-chains 189 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 157 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain D residue 120 LEU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 30 THR Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 428 ILE Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 637 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 73 optimal weight: 5.9990 chunk 50 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 chunk 21 optimal weight: 0.8980 chunk 86 optimal weight: 8.9990 chunk 1 optimal weight: 9.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 83 optimal weight: 6.9990 overall best weight: 1.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.081667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.053835 restraints weight = 55902.483| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.02 r_work: 0.2899 rms_B_bonded: 4.71 restraints_weight: 0.5000 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.6213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14830 Z= 0.167 Angle : 0.580 7.780 21168 Z= 0.324 Chirality : 0.034 0.156 2466 Planarity : 0.003 0.050 1798 Dihedral : 30.801 177.449 4014 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.90 % Favored : 98.01 % Rotamer: Outliers : 2.65 % Allowed : 22.78 % Favored : 74.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.43 (0.25), residues: 1158 helix: 2.81 (0.18), residues: 769 sheet: 0.10 (0.57), residues: 69 loop : -1.18 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 17 TYR 0.010 0.001 TYR D 57 PHE 0.014 0.001 PHE C 62 TRP 0.008 0.001 TRP K 265 HIS 0.003 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (14830) covalent geometry : angle 0.57979 (21168) hydrogen bonds : bond 0.04712 ( 663) hydrogen bonds : angle 3.47647 ( 1862) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 172 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9092 (t0) cc_final: 0.8702 (t0) REVERT: D 113 GLU cc_start: 0.8902 (OUTLIER) cc_final: 0.8573 (mp0) REVERT: D 128 LYS cc_start: 0.9190 (mmmt) cc_final: 0.8909 (mttt) REVERT: C 88 ASP cc_start: 0.9222 (t70) cc_final: 0.8777 (t0) REVERT: C 91 GLU cc_start: 0.9209 (tm-30) cc_final: 0.8931 (tm-30) REVERT: C 96 GLU cc_start: 0.8931 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 113 GLU cc_start: 0.9268 (mp0) cc_final: 0.8957 (mp0) REVERT: C 125 GLU cc_start: 0.8631 (mm-30) cc_final: 0.8286 (tp30) REVERT: F 53 LYS cc_start: 0.8636 (tttt) cc_final: 0.8200 (tppt) REVERT: F 56 LYS cc_start: 0.8525 (tttt) cc_final: 0.8213 (mtpt) REVERT: E 60 LEU cc_start: 0.8799 (mt) cc_final: 0.8534 (mt) REVERT: H 27 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8513 (tm-30) REVERT: H 91 LYS cc_start: 0.9104 (tttt) cc_final: 0.8672 (ttpt) REVERT: A 59 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8959 (mp) REVERT: A 76 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7238 (mtmt) REVERT: A 85 GLN cc_start: 0.9023 (tt0) cc_final: 0.8800 (tt0) REVERT: B 65 GLU cc_start: 0.8905 (tt0) cc_final: 0.8553 (tm-30) outliers start: 23 outliers final: 16 residues processed: 188 average time/residue: 0.1257 time to fit residues: 33.4444 Evaluate side-chains 185 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain K residue 231 LEU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 41 optimal weight: 0.0370 chunk 126 optimal weight: 5.9990 chunk 74 optimal weight: 9.9990 chunk 61 optimal weight: 10.0000 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 112 optimal weight: 30.0000 chunk 83 optimal weight: 6.9990 chunk 89 optimal weight: 0.0670 overall best weight: 2.6202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3805 r_free = 0.3805 target = 0.080842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.052781 restraints weight = 55893.013| |-----------------------------------------------------------------------------| r_work (start): 0.3052 rms_B_bonded: 3.01 r_work: 0.2869 rms_B_bonded: 4.72 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8578 moved from start: 0.6392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 14830 Z= 0.204 Angle : 0.600 8.482 21168 Z= 0.334 Chirality : 0.035 0.155 2466 Planarity : 0.003 0.050 1798 Dihedral : 30.815 176.873 4014 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.34 % Allowed : 23.01 % Favored : 73.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.44 (0.25), residues: 1158 helix: 2.80 (0.18), residues: 771 sheet: 0.23 (0.59), residues: 69 loop : -1.19 (0.30), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 633 TYR 0.011 0.001 TYR D 57 PHE 0.007 0.001 PHE H 61 TRP 0.008 0.001 TRP K 373 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00459 (14830) covalent geometry : angle 0.59973 (21168) hydrogen bonds : bond 0.05256 ( 663) hydrogen bonds : angle 3.59448 ( 1862) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 164 time to evaluate : 0.437 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9112 (t0) cc_final: 0.8735 (t0) REVERT: D 96 GLU cc_start: 0.8807 (mm-30) cc_final: 0.8489 (mm-30) REVERT: D 113 GLU cc_start: 0.8934 (OUTLIER) cc_final: 0.8630 (mp0) REVERT: D 128 LYS cc_start: 0.9181 (mmmt) cc_final: 0.8883 (mttt) REVERT: C 67 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8872 (tm-30) REVERT: C 88 ASP cc_start: 0.9237 (t70) cc_final: 0.8788 (t0) REVERT: C 91 GLU cc_start: 0.9201 (tm-30) cc_final: 0.8934 (tm-30) REVERT: C 113 GLU cc_start: 0.9261 (mp0) cc_final: 0.8946 (mp0) REVERT: C 125 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8312 (tp30) REVERT: F 53 LYS cc_start: 0.8664 (tttt) cc_final: 0.8217 (tppt) REVERT: F 56 LYS cc_start: 0.8496 (tttt) cc_final: 0.8192 (mtpt) REVERT: E 60 LEU cc_start: 0.8735 (mt) cc_final: 0.8341 (mt) REVERT: H 27 GLN cc_start: 0.8941 (tm-30) cc_final: 0.8531 (tm-30) REVERT: H 91 LYS cc_start: 0.9181 (tttt) cc_final: 0.8765 (ttpt) REVERT: A 59 LEU cc_start: 0.9232 (OUTLIER) cc_final: 0.8947 (mp) REVERT: B 65 GLU cc_start: 0.8899 (tt0) cc_final: 0.8525 (tm-30) REVERT: K 229 MET cc_start: 0.8382 (mpp) cc_final: 0.7877 (mtt) REVERT: K 432 MET cc_start: 0.9125 (mmm) cc_final: 0.8287 (tpp) REVERT: K 605 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8203 (pp) outliers start: 29 outliers final: 22 residues processed: 184 average time/residue: 0.1409 time to fit residues: 36.8770 Evaluate side-chains 189 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain F residue 100 LEU Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Chi-restraints excluded: chain K residue 428 ILE Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 637 ILE Chi-restraints excluded: chain K residue 750 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.9990 chunk 125 optimal weight: 7.9990 chunk 116 optimal weight: 50.0000 chunk 1 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 89 optimal weight: 0.0370 chunk 62 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 77 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.2066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 55 GLN E 68 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.082742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.055114 restraints weight = 55723.829| |-----------------------------------------------------------------------------| r_work (start): 0.3106 rms_B_bonded: 3.06 r_work: 0.2926 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.6365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14830 Z= 0.153 Angle : 0.581 12.809 21168 Z= 0.319 Chirality : 0.033 0.150 2466 Planarity : 0.003 0.046 1798 Dihedral : 30.494 176.855 4014 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 3.11 % Allowed : 24.17 % Favored : 72.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.64 (0.25), residues: 1158 helix: 2.93 (0.18), residues: 772 sheet: 0.27 (0.58), residues: 74 loop : -1.09 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 129 TYR 0.011 0.001 TYR G 51 PHE 0.005 0.001 PHE H 61 TRP 0.009 0.001 TRP K 265 HIS 0.003 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00339 (14830) covalent geometry : angle 0.58083 (21168) hydrogen bonds : bond 0.04452 ( 663) hydrogen bonds : angle 3.32579 ( 1862) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9112 (t0) cc_final: 0.8689 (t0) REVERT: D 96 GLU cc_start: 0.8780 (mm-30) cc_final: 0.8488 (mm-30) REVERT: D 128 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8841 (mttt) REVERT: C 88 ASP cc_start: 0.9209 (t70) cc_final: 0.8736 (t0) REVERT: C 91 GLU cc_start: 0.9191 (tm-30) cc_final: 0.8918 (tm-30) REVERT: C 96 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8582 (mm-30) REVERT: C 113 GLU cc_start: 0.9250 (mp0) cc_final: 0.8845 (mp0) REVERT: C 125 GLU cc_start: 0.8544 (mm-30) cc_final: 0.8251 (tp30) REVERT: F 53 LYS cc_start: 0.8656 (tttt) cc_final: 0.8177 (tppt) REVERT: F 55 GLN cc_start: 0.8052 (OUTLIER) cc_final: 0.7660 (mt0) REVERT: F 56 LYS cc_start: 0.8334 (tttt) cc_final: 0.7998 (mtpt) REVERT: F 129 ARG cc_start: 0.9447 (tpp80) cc_final: 0.9200 (ttt180) REVERT: E 60 LEU cc_start: 0.8781 (mt) cc_final: 0.8433 (mt) REVERT: H 27 GLN cc_start: 0.8938 (tm-30) cc_final: 0.8534 (tm-30) REVERT: H 91 LYS cc_start: 0.9117 (tttt) cc_final: 0.8652 (ttpt) REVERT: A 59 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8983 (mp) REVERT: A 76 LYS cc_start: 0.7670 (mmtt) cc_final: 0.7212 (mtmt) REVERT: A 85 GLN cc_start: 0.8990 (tt0) cc_final: 0.8755 (tt0) REVERT: A 92 GLU cc_start: 0.9104 (tp30) cc_final: 0.8852 (tp30) REVERT: B 65 GLU cc_start: 0.8905 (tt0) cc_final: 0.8535 (tm-30) REVERT: K 229 MET cc_start: 0.8220 (mpp) cc_final: 0.7750 (mtt) REVERT: K 432 MET cc_start: 0.9098 (mmm) cc_final: 0.8349 (tpp) outliers start: 27 outliers final: 21 residues processed: 192 average time/residue: 0.1405 time to fit residues: 38.1549 Evaluate side-chains 194 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 171 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain F residue 55 GLN Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 59 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 545 ILE Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 750 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 54 optimal weight: 0.9990 chunk 96 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 44 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 38 optimal weight: 0.6980 chunk 100 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 95 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 125 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.083616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.055695 restraints weight = 56521.427| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 3.09 r_work: 0.2941 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.6379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 14830 Z= 0.148 Angle : 0.588 12.533 21168 Z= 0.321 Chirality : 0.033 0.149 2466 Planarity : 0.003 0.046 1798 Dihedral : 30.433 176.839 4014 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 3.22 % Allowed : 23.82 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.68 (0.25), residues: 1158 helix: 2.97 (0.18), residues: 769 sheet: 0.41 (0.59), residues: 74 loop : -1.08 (0.31), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 72 TYR 0.012 0.001 TYR B 51 PHE 0.009 0.001 PHE C 62 TRP 0.009 0.001 TRP K 265 HIS 0.004 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00326 (14830) covalent geometry : angle 0.58766 (21168) hydrogen bonds : bond 0.04434 ( 663) hydrogen bonds : angle 3.26860 ( 1862) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 178 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9115 (t0) cc_final: 0.8684 (t0) REVERT: D 96 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8501 (mm-30) REVERT: D 128 LYS cc_start: 0.9130 (mmmt) cc_final: 0.8829 (mttt) REVERT: C 67 GLN cc_start: 0.9090 (tm-30) cc_final: 0.8859 (tm-30) REVERT: C 88 ASP cc_start: 0.9168 (t70) cc_final: 0.8705 (t0) REVERT: C 91 GLU cc_start: 0.9157 (tm-30) cc_final: 0.8875 (tm-30) REVERT: C 96 GLU cc_start: 0.8909 (mm-30) cc_final: 0.8550 (mm-30) REVERT: C 125 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8197 (tp30) REVERT: F 53 LYS cc_start: 0.8630 (tttt) cc_final: 0.8166 (tppt) REVERT: F 56 LYS cc_start: 0.8271 (tttt) cc_final: 0.7958 (mtpt) REVERT: F 129 ARG cc_start: 0.9445 (tpp80) cc_final: 0.9209 (ttt180) REVERT: E 60 LEU cc_start: 0.8804 (mt) cc_final: 0.8485 (mt) REVERT: H 27 GLN cc_start: 0.8900 (tm-30) cc_final: 0.8510 (tm-30) REVERT: H 91 LYS cc_start: 0.9150 (tttt) cc_final: 0.8661 (ttpt) REVERT: A 34 PHE cc_start: 0.9311 (m-80) cc_final: 0.9079 (m-80) REVERT: A 85 GLN cc_start: 0.9018 (tt0) cc_final: 0.8747 (tt0) REVERT: A 92 GLU cc_start: 0.9107 (tp30) cc_final: 0.8842 (tp30) REVERT: B 62 GLU cc_start: 0.9020 (tt0) cc_final: 0.8780 (tt0) REVERT: B 65 GLU cc_start: 0.8898 (tt0) cc_final: 0.8555 (tm-30) REVERT: K 229 MET cc_start: 0.8239 (mpp) cc_final: 0.7752 (mtt) REVERT: K 432 MET cc_start: 0.9106 (mmm) cc_final: 0.8360 (tpp) REVERT: K 605 LEU cc_start: 0.8397 (OUTLIER) cc_final: 0.8170 (pp) outliers start: 28 outliers final: 23 residues processed: 197 average time/residue: 0.1398 time to fit residues: 38.5917 Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 545 ILE Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 0 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 110 optimal weight: 4.9990 chunk 118 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 122 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 100 optimal weight: 4.9990 chunk 2 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.082770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.054612 restraints weight = 56908.316| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 3.11 r_work: 0.2915 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.6515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14830 Z= 0.169 Angle : 0.596 12.460 21168 Z= 0.326 Chirality : 0.034 0.155 2466 Planarity : 0.003 0.048 1798 Dihedral : 30.482 176.710 4014 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.88 % Allowed : 24.51 % Favored : 72.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.71 (0.25), residues: 1158 helix: 2.95 (0.18), residues: 771 sheet: 0.45 (0.59), residues: 74 loop : -0.98 (0.32), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 72 TYR 0.012 0.001 TYR B 51 PHE 0.008 0.001 PHE E 104 TRP 0.007 0.001 TRP K 373 HIS 0.006 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00379 (14830) covalent geometry : angle 0.59564 (21168) hydrogen bonds : bond 0.04736 ( 663) hydrogen bonds : angle 3.35152 ( 1862) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2316 Ramachandran restraints generated. 1158 Oldfield, 0 Emsley, 1158 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 167 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 77 LYS cc_start: 0.9213 (mtpp) cc_final: 0.8961 (mtmm) REVERT: D 88 ASP cc_start: 0.9115 (t0) cc_final: 0.8699 (t0) REVERT: D 96 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8474 (mm-30) REVERT: D 128 LYS cc_start: 0.9149 (mmmt) cc_final: 0.8848 (mttt) REVERT: C 67 GLN cc_start: 0.9094 (tm-30) cc_final: 0.8854 (tm-30) REVERT: C 88 ASP cc_start: 0.9205 (t70) cc_final: 0.8742 (t0) REVERT: C 91 GLU cc_start: 0.9183 (tm-30) cc_final: 0.8904 (tm-30) REVERT: C 96 GLU cc_start: 0.8929 (mm-30) cc_final: 0.8533 (mm-30) REVERT: C 113 GLU cc_start: 0.9255 (mp0) cc_final: 0.8848 (mp0) REVERT: C 125 GLU cc_start: 0.8530 (mm-30) cc_final: 0.8223 (tp30) REVERT: F 53 LYS cc_start: 0.8661 (tttt) cc_final: 0.8204 (tppt) REVERT: F 56 LYS cc_start: 0.8303 (tttt) cc_final: 0.7923 (mtpt) REVERT: E 60 LEU cc_start: 0.8710 (mt) cc_final: 0.8403 (mt) REVERT: H 27 GLN cc_start: 0.8934 (tm-30) cc_final: 0.8543 (tm-30) REVERT: H 91 LYS cc_start: 0.9163 (tttt) cc_final: 0.8710 (ttpt) REVERT: A 34 PHE cc_start: 0.9323 (m-80) cc_final: 0.9089 (m-80) REVERT: A 76 LYS cc_start: 0.7747 (mmtt) cc_final: 0.7250 (mtmt) REVERT: A 85 GLN cc_start: 0.9014 (tt0) cc_final: 0.8766 (tt0) REVERT: A 92 GLU cc_start: 0.9108 (tp30) cc_final: 0.8842 (tp30) REVERT: B 65 GLU cc_start: 0.8898 (tt0) cc_final: 0.8550 (tm-30) REVERT: K 229 MET cc_start: 0.8231 (mpp) cc_final: 0.7763 (mtt) REVERT: K 432 MET cc_start: 0.9121 (mmm) cc_final: 0.8391 (tpp) REVERT: K 605 LEU cc_start: 0.8386 (OUTLIER) cc_final: 0.8136 (pp) outliers start: 25 outliers final: 23 residues processed: 183 average time/residue: 0.1240 time to fit residues: 32.1635 Evaluate side-chains 189 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 165 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 86 ILE Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 104 PHE Chi-restraints excluded: chain E residue 110 CYS Chi-restraints excluded: chain E residue 131 ARG Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 50 VAL Chi-restraints excluded: chain K residue 225 LEU Chi-restraints excluded: chain K residue 309 THR Chi-restraints excluded: chain K residue 330 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 428 ILE Chi-restraints excluded: chain K residue 545 ILE Chi-restraints excluded: chain K residue 605 LEU Chi-restraints excluded: chain K residue 615 CYS Chi-restraints excluded: chain K residue 750 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 50 optimal weight: 10.0000 chunk 79 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 74 optimal weight: 8.9990 chunk 94 optimal weight: 9.9990 chunk 83 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 117 optimal weight: 0.0010 chunk 73 optimal weight: 5.9990 overall best weight: 2.1792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 55 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.082287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054132 restraints weight = 56275.443| |-----------------------------------------------------------------------------| r_work (start): 0.3075 rms_B_bonded: 3.07 r_work: 0.2895 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.6703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14830 Z= 0.185 Angle : 0.603 12.388 21168 Z= 0.331 Chirality : 0.034 0.159 2466 Planarity : 0.003 0.049 1798 Dihedral : 30.569 176.457 4014 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.76 % Allowed : 24.74 % Favored : 72.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.65 (0.25), residues: 1158 helix: 2.91 (0.18), residues: 771 sheet: 0.51 (0.59), residues: 68 loop : -1.00 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 72 TYR 0.010 0.001 TYR D 57 PHE 0.008 0.001 PHE C 62 TRP 0.008 0.001 TRP K 373 HIS 0.005 0.001 HIS H 75 Details of bonding type rmsd covalent geometry : bond 0.00416 (14830) covalent geometry : angle 0.60329 (21168) hydrogen bonds : bond 0.04935 ( 663) hydrogen bonds : angle 3.42357 ( 1862) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3823.18 seconds wall clock time: 65 minutes 56.13 seconds (3956.13 seconds total)