Starting phenix.real_space_refine on Fri May 16 01:09:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8kcb_37098/05_2025/8kcb_37098.cif Found real_map, /net/cci-nas-00/data/ceres_data/8kcb_37098/05_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8kcb_37098/05_2025/8kcb_37098.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8kcb_37098/05_2025/8kcb_37098.map" model { file = "/net/cci-nas-00/data/ceres_data/8kcb_37098/05_2025/8kcb_37098.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8kcb_37098/05_2025/8kcb_37098.cif" } resolution = 3.17 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'GLU:plan': 3, 'ARG: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: {'GLU:plan': 3, 'ARG:plan': 4, '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: {'GLN:plan1': 11, 'ARG:plan': 8, 'TYR:plan': 3, 'ASN:plan1': 4, 'TRP:plan': 1, 'ASP:plan': 15, 'PHE:plan': 7, 'GLU:plan': 12, 'HIS:plan': 5} 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: 8.80, per 1000 atoms: 0.63 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: 3.29 Conformation dependent library (CDL) restraints added in 1.3 seconds 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: 5.19 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: 5.71 Time building geometry restraints manager: 3.90 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: 1.470 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: 0.020 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.140 Process input model: 36.860 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.070 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.004 0.000 TRP K 373 HIS 0.004 0.001 HIS H 18 PHE 0.005 0.001 PHE C 90 TYR 0.020 0.001 TYR G 72 ARG 0.005 0.000 ARG G 92 Details of bonding type rmsd hydrogen bonds : bond 0.18793 ( 663) hydrogen bonds : angle 6.52089 ( 1862) covalent geometry : bond 0.00452 (14830) covalent geometry : angle 0.57057 (21168) *********************** 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 : 1.130 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: 0.3673 time to fit residues: 140.8286 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 : 1.228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 114 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 57 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 55 optimal weight: 10.0000 chunk 106 optimal weight: 0.8980 chunk 41 optimal weight: 8.9990 chunk 64 optimal weight: 10.0000 chunk 79 optimal weight: 5.9990 chunk 123 optimal weight: 2.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 = 0.3886 r_free = 0.3886 target = 0.086927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.058584 restraints weight = 55721.667| |-----------------------------------------------------------------------------| r_work (start): 0.3163 rms_B_bonded: 3.24 r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 14830 Z= 0.280 Angle : 0.662 6.590 21168 Z= 0.371 Chirality : 0.038 0.157 2466 Planarity : 0.005 0.047 1798 Dihedral : 30.870 179.085 4014 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.07 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.30 % Favored : 98.62 % Rotamer: Outliers : 2.99 % Allowed : 14.15 % Favored : 82.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.23), residues: 1158 helix: 1.67 (0.18), residues: 763 sheet: -0.05 (0.59), residues: 64 loop : -1.58 (0.28), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 622 HIS 0.010 0.001 HIS C 69 PHE 0.010 0.001 PHE C 85 TYR 0.012 0.002 TYR G 98 ARG 0.006 0.001 ARG G 35 Details of bonding type rmsd hydrogen bonds : bond 0.06454 ( 663) hydrogen bonds : angle 3.89289 ( 1862) covalent geometry : bond 0.00620 (14830) covalent geometry : angle 0.66168 (21168) *********************** 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 208 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 182 time to evaluate : 1.193 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.8910 (t0) cc_final: 0.8552 (t0) REVERT: C 71 ASP cc_start: 0.8837 (p0) cc_final: 0.8560 (p0) REVERT: C 88 ASP cc_start: 0.9126 (t0) cc_final: 0.8680 (t0) REVERT: C 91 GLU cc_start: 0.8855 (tm-30) cc_final: 0.8542 (tm-30) REVERT: C 96 GLU cc_start: 0.8524 (mm-30) cc_final: 0.8111 (mm-30) REVERT: C 125 GLU cc_start: 0.8472 (mm-30) cc_final: 0.8083 (tp30) REVERT: F 53 LYS cc_start: 0.8595 (tttt) cc_final: 0.8375 (tppt) REVERT: F 56 LYS cc_start: 0.8482 (tttt) cc_final: 0.8228 (mtpt) REVERT: F 86 SER cc_start: 0.9210 (m) cc_final: 0.8987 (p) REVERT: E 60 LEU cc_start: 0.8966 (mt) cc_final: 0.8763 (mm) REVERT: E 97 GLU cc_start: 0.8081 (tt0) cc_final: 0.7728 (tt0) REVERT: H 27 GLN cc_start: 0.8411 (tm-30) cc_final: 0.8148 (tm-30) REVERT: H 91 LYS cc_start: 0.9264 (tttt) cc_final: 0.8746 (ttpt) REVERT: A 85 GLN cc_start: 0.9078 (tt0) cc_final: 0.8757 (tt0) REVERT: B 62 GLU cc_start: 0.8739 (tt0) cc_final: 0.8486 (tt0) REVERT: B 65 GLU cc_start: 0.8618 (tt0) cc_final: 0.8274 (tm-30) REVERT: K 315 MET cc_start: 0.9101 (ttp) cc_final: 0.8812 (ttt) REVERT: K 571 ASP cc_start: 0.7953 (t0) cc_final: 0.7636 (t0) outliers start: 26 outliers final: 11 residues processed: 197 average time/residue: 0.2795 time to fit residues: 77.8194 Evaluate side-chains 169 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 158 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain C residue 118 VAL 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 96 THR Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain B residue 80 VAL Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 70 optimal weight: 5.9990 chunk 77 optimal weight: 10.0000 chunk 84 optimal weight: 7.9990 chunk 42 optimal weight: 0.8980 chunk 100 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 66 optimal weight: 10.0000 chunk 120 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 131 optimal weight: 4.9990 overall best weight: 3.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.084557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.056145 restraints weight = 56312.723| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.21 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.4683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14830 Z= 0.224 Angle : 0.589 7.027 21168 Z= 0.332 Chirality : 0.035 0.153 2466 Planarity : 0.004 0.048 1798 Dihedral : 30.704 178.888 4014 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.38 % Favored : 98.53 % Rotamer: Outliers : 2.42 % Allowed : 16.92 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.24), residues: 1158 helix: 2.44 (0.18), residues: 757 sheet: 0.22 (0.58), residues: 67 loop : -1.32 (0.29), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 549 HIS 0.007 0.001 HIS G 75 PHE 0.009 0.001 PHE D 141 TYR 0.014 0.001 TYR K 311 ARG 0.005 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05573 ( 663) hydrogen bonds : angle 3.61331 ( 1862) covalent geometry : bond 0.00507 (14830) covalent geometry : angle 0.58925 (21168) *********************** 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: 21 poor density : 172 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 58 LYS cc_start: 0.8922 (mmtp) cc_final: 0.8700 (mmtm) REVERT: D 88 ASP cc_start: 0.9032 (t0) cc_final: 0.8643 (t0) REVERT: D 128 LYS cc_start: 0.9046 (mmmt) cc_final: 0.8756 (mttt) REVERT: C 67 GLN cc_start: 0.9060 (tm-30) cc_final: 0.8833 (tm-30) REVERT: C 79 MET cc_start: 0.8949 (tpp) cc_final: 0.8665 (tpp) REVERT: C 88 ASP cc_start: 0.9136 (t0) cc_final: 0.8625 (t0) REVERT: C 91 GLU cc_start: 0.8899 (tm-30) cc_final: 0.8576 (tm-30) REVERT: C 96 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8096 (mm-30) REVERT: C 125 GLU cc_start: 0.8388 (mm-30) cc_final: 0.7998 (tp30) REVERT: C 133 GLU cc_start: 0.9164 (mm-30) cc_final: 0.8959 (tp30) REVERT: F 53 LYS cc_start: 0.8587 (tttt) cc_final: 0.8355 (tppt) REVERT: F 56 LYS cc_start: 0.8559 (tttt) cc_final: 0.8279 (mtpt) REVERT: F 86 SER cc_start: 0.9118 (m) cc_final: 0.8910 (p) REVERT: E 60 LEU cc_start: 0.9073 (mt) cc_final: 0.8645 (mt) REVERT: E 97 GLU cc_start: 0.8065 (tt0) cc_final: 0.7488 (tt0) REVERT: H 27 GLN cc_start: 0.8533 (tm-30) cc_final: 0.8191 (tm-30) REVERT: H 91 LYS cc_start: 0.9150 (tttt) cc_final: 0.8709 (ttpt) REVERT: A 59 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8784 (mp) REVERT: A 91 ASP cc_start: 0.8674 (t0) cc_final: 0.8457 (t0) REVERT: A 92 GLU cc_start: 0.9094 (tp30) cc_final: 0.8782 (tp30) REVERT: A 96 LYS cc_start: 0.8788 (mttt) cc_final: 0.8301 (mttt) REVERT: B 62 GLU cc_start: 0.8740 (tt0) cc_final: 0.8482 (tt0) REVERT: B 65 GLU cc_start: 0.8628 (tt0) cc_final: 0.8268 (tm-30) REVERT: K 548 GLN cc_start: 0.8958 (OUTLIER) cc_final: 0.8557 (pp30) outliers start: 21 outliers final: 13 residues processed: 186 average time/residue: 0.2839 time to fit residues: 74.8166 Evaluate side-chains 177 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 162 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 74 ILE Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR 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 A residue 59 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 48 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 chunk 66 optimal weight: 7.9990 chunk 100 optimal weight: 4.9990 chunk 27 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 108 optimal weight: 20.0000 chunk 67 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 77 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.082219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.053621 restraints weight = 56676.963| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 3.10 r_work: 0.2872 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.5505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 14830 Z= 0.239 Angle : 0.595 6.843 21168 Z= 0.337 Chirality : 0.036 0.148 2466 Planarity : 0.004 0.052 1798 Dihedral : 30.848 178.306 4014 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.17 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer: Outliers : 3.34 % Allowed : 18.64 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.17 (0.24), residues: 1158 helix: 2.55 (0.18), residues: 774 sheet: 0.33 (0.58), residues: 67 loop : -1.25 (0.30), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 373 HIS 0.006 0.001 HIS G 75 PHE 0.008 0.001 PHE E 104 TYR 0.010 0.001 TYR D 57 ARG 0.007 0.001 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.05703 ( 663) hydrogen bonds : angle 3.69023 ( 1862) covalent geometry : bond 0.00539 (14830) covalent geometry : angle 0.59511 (21168) *********************** 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 198 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 169 time to evaluate : 1.150 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9098 (t0) cc_final: 0.8777 (t0) REVERT: D 113 GLU cc_start: 0.8928 (OUTLIER) cc_final: 0.8636 (mp0) REVERT: D 128 LYS cc_start: 0.9173 (mmmt) cc_final: 0.8899 (mttt) REVERT: C 67 GLN cc_start: 0.9160 (tm-30) cc_final: 0.8935 (tm-30) REVERT: C 79 MET cc_start: 0.9154 (tpp) cc_final: 0.8915 (tpp) REVERT: C 88 ASP cc_start: 0.9285 (t70) cc_final: 0.8796 (t0) REVERT: C 91 GLU cc_start: 0.9222 (tm-30) cc_final: 0.8917 (tm-30) REVERT: C 125 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8411 (tp30) REVERT: C 133 GLU cc_start: 0.9281 (mm-30) cc_final: 0.9006 (tp30) REVERT: F 53 LYS cc_start: 0.8596 (tttt) cc_final: 0.8300 (tppt) REVERT: F 55 GLN cc_start: 0.7943 (mt0) cc_final: 0.7490 (mp10) REVERT: F 56 LYS cc_start: 0.8620 (tttt) cc_final: 0.8318 (mtpt) REVERT: E 60 LEU cc_start: 0.8854 (mt) cc_final: 0.8323 (mt) REVERT: E 97 GLU cc_start: 0.8693 (tt0) cc_final: 0.8251 (tt0) REVERT: H 27 GLN cc_start: 0.8882 (tm-30) cc_final: 0.8509 (tm-30) REVERT: H 91 LYS cc_start: 0.9254 (tttt) cc_final: 0.8908 (ttpt) REVERT: A 76 LYS cc_start: 0.7795 (mmtt) cc_final: 0.7378 (mtmt) REVERT: A 85 GLN cc_start: 0.9098 (tt0) cc_final: 0.8883 (tt0) REVERT: A 92 GLU cc_start: 0.9067 (tp30) cc_final: 0.8754 (tp30) REVERT: A 94 LEU cc_start: 0.9611 (OUTLIER) cc_final: 0.9395 (tt) REVERT: A 96 LYS cc_start: 0.8911 (mttt) cc_final: 0.8414 (mttt) REVERT: B 65 GLU cc_start: 0.8918 (tt0) cc_final: 0.8550 (tm-30) REVERT: K 432 MET cc_start: 0.9078 (mmm) cc_final: 0.8350 (tpp) REVERT: K 548 GLN cc_start: 0.9083 (OUTLIER) cc_final: 0.8674 (pp30) REVERT: K 605 LEU cc_start: 0.8555 (OUTLIER) cc_final: 0.8296 (pp) outliers start: 29 outliers final: 17 residues processed: 192 average time/residue: 0.2816 time to fit residues: 76.2968 Evaluate side-chains 181 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 108 THR Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain C residue 74 ILE Chi-restraints excluded: chain C residue 118 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain E residue 58 THR 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 94 LEU Chi-restraints excluded: chain B residue 80 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 98 optimal weight: 0.1980 chunk 112 optimal weight: 8.9990 chunk 63 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 83 ASN F 55 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.084071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.055846 restraints weight = 56396.120| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.06 r_work: 0.2945 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 14830 Z= 0.150 Angle : 0.552 7.476 21168 Z= 0.310 Chirality : 0.033 0.235 2466 Planarity : 0.003 0.050 1798 Dihedral : 30.587 178.048 4014 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 1.64 % Favored : 98.27 % Rotamer: Outliers : 3.11 % Allowed : 19.68 % Favored : 77.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.56 (0.25), residues: 1158 helix: 2.94 (0.18), residues: 759 sheet: 0.52 (0.60), residues: 67 loop : -1.16 (0.30), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 265 HIS 0.004 0.001 HIS G 75 PHE 0.008 0.001 PHE E 104 TYR 0.010 0.001 TYR G 51 ARG 0.004 0.000 ARG A 89 Details of bonding type rmsd hydrogen bonds : bond 0.04588 ( 663) hydrogen bonds : angle 3.31371 ( 1862) covalent geometry : bond 0.00333 (14830) covalent geometry : angle 0.55187 (21168) *********************** 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 206 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.988 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9045 (t0) cc_final: 0.8715 (t0) REVERT: D 128 LYS cc_start: 0.9104 (mmmt) cc_final: 0.8825 (mttt) REVERT: C 67 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8888 (tm-30) REVERT: C 79 MET cc_start: 0.9084 (tpp) cc_final: 0.8774 (tpp) REVERT: C 88 ASP cc_start: 0.9206 (t70) cc_final: 0.8761 (t0) REVERT: C 91 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8906 (tm-30) REVERT: C 96 GLU cc_start: 0.8902 (mm-30) cc_final: 0.8424 (mm-30) REVERT: C 113 GLU cc_start: 0.9267 (mp0) cc_final: 0.9030 (mp0) REVERT: C 125 GLU cc_start: 0.8591 (mm-30) cc_final: 0.8305 (tp30) REVERT: C 133 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8941 (tp30) REVERT: F 53 LYS cc_start: 0.8684 (tttt) cc_final: 0.8372 (tppt) REVERT: F 56 LYS cc_start: 0.8632 (tttt) cc_final: 0.8336 (mtpt) REVERT: F 133 GLU cc_start: 0.8850 (pt0) cc_final: 0.8595 (pt0) REVERT: E 60 LEU cc_start: 0.8907 (mt) cc_final: 0.8449 (mt) REVERT: E 97 GLU cc_start: 0.8656 (tt0) cc_final: 0.8173 (tt0) REVERT: H 27 GLN cc_start: 0.8855 (tm-30) cc_final: 0.8429 (tm-30) REVERT: H 91 LYS cc_start: 0.9206 (tttt) cc_final: 0.8797 (ttpt) REVERT: A 76 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7194 (mtmt) REVERT: A 92 GLU cc_start: 0.9068 (tp30) cc_final: 0.8825 (tp30) REVERT: A 96 LYS cc_start: 0.8900 (mttt) cc_final: 0.8574 (mttt) REVERT: B 65 GLU cc_start: 0.8901 (tt0) cc_final: 0.8545 (tm-30) REVERT: K 231 LEU cc_start: 0.7982 (OUTLIER) cc_final: 0.7646 (tt) outliers start: 27 outliers final: 17 residues processed: 197 average time/residue: 0.3123 time to fit residues: 85.2187 Evaluate side-chains 187 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 1.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER 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 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 82 THR Chi-restraints excluded: chain H residue 96 THR Chi-restraints excluded: chain G residue 93 GLN Chi-restraints excluded: chain A residue 101 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 615 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 3 optimal weight: 0.9990 chunk 49 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 79 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 125 optimal weight: 0.8980 chunk 107 optimal weight: 0.9990 chunk 123 optimal weight: 5.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 125 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.085014 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056799 restraints weight = 56505.917| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.12 r_work: 0.2957 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.5592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 14830 Z= 0.143 Angle : 0.561 8.520 21168 Z= 0.310 Chirality : 0.033 0.154 2466 Planarity : 0.004 0.051 1798 Dihedral : 30.462 178.315 4014 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.07 % Allowed : 20.60 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.25), residues: 1158 helix: 3.05 (0.18), residues: 766 sheet: 0.58 (0.61), residues: 69 loop : -1.13 (0.29), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 549 HIS 0.003 0.001 HIS G 75 PHE 0.017 0.001 PHE C 62 TYR 0.011 0.001 TYR K 513 ARG 0.007 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04517 ( 663) hydrogen bonds : angle 3.21029 ( 1862) covalent geometry : bond 0.00314 (14830) covalent geometry : angle 0.56130 (21168) *********************** 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: 18 poor density : 177 time to evaluate : 1.263 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 79 MET cc_start: 0.7967 (tpp) cc_final: 0.7668 (tpp) REVERT: D 88 ASP cc_start: 0.9079 (t0) cc_final: 0.8691 (t0) REVERT: D 96 GLU cc_start: 0.8758 (mm-30) cc_final: 0.8480 (mm-30) REVERT: D 128 LYS cc_start: 0.9094 (mmmt) cc_final: 0.8817 (mttt) REVERT: C 67 GLN cc_start: 0.9178 (tm-30) cc_final: 0.8901 (tm-30) REVERT: C 79 MET cc_start: 0.9051 (tpp) cc_final: 0.8711 (tpp) REVERT: C 88 ASP cc_start: 0.9225 (t70) cc_final: 0.8766 (t0) REVERT: C 91 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8915 (tm-30) REVERT: C 113 GLU cc_start: 0.9260 (mp0) cc_final: 0.8940 (mp0) REVERT: C 125 GLU cc_start: 0.8488 (mm-30) cc_final: 0.8231 (tp30) REVERT: C 133 GLU cc_start: 0.9249 (mm-30) cc_final: 0.9020 (tp30) REVERT: F 53 LYS cc_start: 0.8665 (tttt) cc_final: 0.8264 (tppt) REVERT: F 55 GLN cc_start: 0.7875 (mt0) cc_final: 0.7618 (mp10) REVERT: F 56 LYS cc_start: 0.8585 (tttt) cc_final: 0.8319 (mtpt) REVERT: E 60 LEU cc_start: 0.8934 (mt) cc_final: 0.8568 (mt) REVERT: E 97 GLU cc_start: 0.8674 (tt0) cc_final: 0.8152 (tt0) REVERT: H 27 GLN cc_start: 0.8877 (tm-30) cc_final: 0.8466 (tm-30) REVERT: H 91 LYS cc_start: 0.9217 (tttt) cc_final: 0.8742 (ttpt) REVERT: A 96 LYS cc_start: 0.8903 (mttt) cc_final: 0.8607 (mttt) REVERT: B 65 GLU cc_start: 0.8899 (tt0) cc_final: 0.8568 (tm-30) REVERT: K 231 LEU cc_start: 0.7785 (OUTLIER) cc_final: 0.7419 (tt) REVERT: K 432 MET cc_start: 0.9055 (mmm) cc_final: 0.8302 (tpp) outliers start: 18 outliers final: 14 residues processed: 189 average time/residue: 0.3096 time to fit residues: 82.1973 Evaluate side-chains 182 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 167 time to evaluate : 1.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D 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 80 THR Chi-restraints excluded: chain E residue 82 LEU 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 K residue 231 LEU Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 615 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 89 optimal weight: 0.0980 chunk 6 optimal weight: 2.9990 chunk 95 optimal weight: 9.9990 chunk 78 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 10.0000 chunk 48 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.082623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.054441 restraints weight = 55951.319| |-----------------------------------------------------------------------------| r_work (start): 0.3078 rms_B_bonded: 3.06 r_work: 0.2895 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.5941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14830 Z= 0.209 Angle : 0.596 8.493 21168 Z= 0.331 Chirality : 0.035 0.161 2466 Planarity : 0.004 0.050 1798 Dihedral : 30.636 177.281 4014 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.65 % Allowed : 21.52 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.67 (0.25), residues: 1158 helix: 2.91 (0.18), residues: 774 sheet: 0.87 (0.63), residues: 64 loop : -1.09 (0.30), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 549 HIS 0.005 0.001 HIS H 75 PHE 0.010 0.001 PHE E 104 TYR 0.011 0.001 TYR B 51 ARG 0.004 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05336 ( 663) hydrogen bonds : angle 3.52171 ( 1862) covalent geometry : bond 0.00470 (14830) covalent geometry : angle 0.59566 (21168) *********************** 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 185 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 162 time to evaluate : 1.099 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9043 (t0) cc_final: 0.8700 (t0) REVERT: C 67 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 79 MET cc_start: 0.9153 (tpp) cc_final: 0.8814 (tpp) REVERT: C 88 ASP cc_start: 0.9236 (t70) cc_final: 0.8719 (t0) REVERT: C 91 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8921 (tm-30) REVERT: C 96 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8553 (mm-30) REVERT: C 113 GLU cc_start: 0.9256 (mp0) cc_final: 0.9013 (mp0) REVERT: C 125 GLU cc_start: 0.8651 (mm-30) cc_final: 0.8411 (tp30) REVERT: C 133 GLU cc_start: 0.9223 (mm-30) cc_final: 0.8998 (tp30) REVERT: F 55 GLN cc_start: 0.8129 (mt0) cc_final: 0.7596 (mp10) REVERT: F 56 LYS cc_start: 0.8485 (tttt) cc_final: 0.8240 (mtpt) REVERT: F 59 GLU cc_start: 0.7387 (pt0) cc_final: 0.6310 (pm20) REVERT: E 60 LEU cc_start: 0.8837 (mt) cc_final: 0.8368 (mt) REVERT: E 61 LEU cc_start: 0.8445 (mt) cc_final: 0.8214 (mt) REVERT: E 97 GLU cc_start: 0.8728 (tt0) cc_final: 0.8122 (tt0) REVERT: H 27 GLN cc_start: 0.8937 (tm-30) cc_final: 0.8502 (tm-30) REVERT: H 91 LYS cc_start: 0.9245 (tttt) cc_final: 0.8845 (ttpt) REVERT: A 76 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7412 (mtmt) REVERT: B 65 GLU cc_start: 0.8899 (tt0) cc_final: 0.8539 (tm-30) REVERT: K 229 MET cc_start: 0.8532 (mpp) cc_final: 0.7571 (mtt) REVERT: K 231 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7795 (tt) REVERT: K 432 MET cc_start: 0.9014 (mmm) cc_final: 0.8287 (tpp) outliers start: 23 outliers final: 18 residues processed: 177 average time/residue: 0.2818 time to fit residues: 70.0726 Evaluate side-chains 178 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain C residue 76 SER 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 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 88 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 615 CYS Chi-restraints excluded: chain K residue 637 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 20.0000 chunk 93 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 102 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 122 optimal weight: 9.9990 chunk 37 optimal weight: 0.8980 chunk 50 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 108 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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 = 0.3828 r_free = 0.3828 target = 0.082431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054238 restraints weight = 56530.254| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 3.06 r_work: 0.2901 rms_B_bonded: 4.79 restraints_weight: 0.5000 r_work (final): 0.2901 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.6161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 14830 Z= 0.198 Angle : 0.595 8.156 21168 Z= 0.330 Chirality : 0.034 0.153 2466 Planarity : 0.003 0.050 1798 Dihedral : 30.618 176.844 4014 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.65 % Allowed : 21.63 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.68 (0.25), residues: 1158 helix: 2.94 (0.18), residues: 772 sheet: 0.47 (0.59), residues: 74 loop : -1.07 (0.31), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 373 HIS 0.005 0.001 HIS H 75 PHE 0.012 0.001 PHE C 62 TYR 0.011 0.001 TYR G 51 ARG 0.003 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 663) hydrogen bonds : angle 3.45242 ( 1862) covalent geometry : bond 0.00447 (14830) covalent geometry : angle 0.59506 (21168) *********************** 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 186 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.148 Fit side-chains revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9114 (t0) cc_final: 0.8728 (t0) REVERT: D 96 GLU cc_start: 0.8865 (mm-30) cc_final: 0.8595 (mm-30) REVERT: D 133 GLU cc_start: 0.8914 (tt0) cc_final: 0.8693 (tt0) REVERT: C 67 GLN cc_start: 0.9166 (tm-30) cc_final: 0.8889 (tm-30) REVERT: C 79 MET cc_start: 0.9133 (tpp) cc_final: 0.8779 (tpp) REVERT: C 88 ASP cc_start: 0.9259 (t70) cc_final: 0.8714 (t0) REVERT: C 91 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8908 (tm-30) REVERT: C 96 GLU cc_start: 0.8933 (mm-30) cc_final: 0.8532 (mm-30) REVERT: C 113 GLU cc_start: 0.9300 (mp0) cc_final: 0.9053 (mp0) REVERT: C 125 GLU cc_start: 0.8689 (mm-30) cc_final: 0.8380 (tp30) REVERT: C 133 GLU cc_start: 0.9280 (mm-30) cc_final: 0.9048 (tp30) REVERT: F 55 GLN cc_start: 0.8076 (mt0) cc_final: 0.7420 (mt0) REVERT: F 56 LYS cc_start: 0.8417 (tttt) cc_final: 0.8162 (mtpt) REVERT: E 60 LEU cc_start: 0.8840 (mt) cc_final: 0.8399 (mt) REVERT: E 61 LEU cc_start: 0.8435 (mt) cc_final: 0.8201 (mt) REVERT: E 97 GLU cc_start: 0.8734 (tt0) cc_final: 0.8158 (tt0) REVERT: H 27 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8559 (tm-30) REVERT: H 91 LYS cc_start: 0.9198 (tttt) cc_final: 0.8806 (ttpt) REVERT: G 79 LYS cc_start: 0.8668 (mmtt) cc_final: 0.8451 (mmmm) REVERT: A 76 LYS cc_start: 0.7849 (mmtt) cc_final: 0.7382 (mtmt) REVERT: A 92 GLU cc_start: 0.9064 (tp30) cc_final: 0.8714 (tp30) REVERT: A 94 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9322 (mt) REVERT: B 65 GLU cc_start: 0.8910 (tt0) cc_final: 0.8546 (tm-30) REVERT: K 229 MET cc_start: 0.8487 (mpp) cc_final: 0.7572 (mtt) REVERT: K 432 MET cc_start: 0.9024 (mmm) cc_final: 0.8313 (tpp) outliers start: 23 outliers final: 20 residues processed: 178 average time/residue: 0.2934 time to fit residues: 73.4766 Evaluate side-chains 181 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 160 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 76 SER Chi-restraints excluded: chain C residue 76 SER 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 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 88 VAL Chi-restraints excluded: chain A residue 94 LEU Chi-restraints excluded: chain A residue 101 VAL 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 615 CYS Chi-restraints excluded: chain K residue 637 ILE 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 83 optimal weight: 6.9990 chunk 5 optimal weight: 0.0470 chunk 73 optimal weight: 6.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 104 optimal weight: 0.0980 chunk 62 optimal weight: 8.9990 chunk 82 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.085011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.057135 restraints weight = 56158.877| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 3.12 r_work: 0.2981 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.2981 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 14830 Z= 0.141 Angle : 0.582 13.884 21168 Z= 0.316 Chirality : 0.033 0.269 2466 Planarity : 0.003 0.046 1798 Dihedral : 30.334 177.349 4014 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 1.50 % Allowed : 22.90 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.88 (0.25), residues: 1158 helix: 3.09 (0.18), residues: 770 sheet: 0.75 (0.62), residues: 68 loop : -0.98 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 265 HIS 0.004 0.001 HIS H 75 PHE 0.007 0.001 PHE E 104 TYR 0.013 0.001 TYR B 51 ARG 0.004 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 663) hydrogen bonds : angle 3.20110 ( 1862) covalent geometry : bond 0.00307 (14830) covalent geometry : angle 0.58205 (21168) *********************** 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 190 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 177 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 79 MET cc_start: 0.8063 (tpp) cc_final: 0.7745 (tpp) REVERT: D 88 ASP cc_start: 0.9101 (t0) cc_final: 0.8669 (t0) REVERT: D 96 GLU cc_start: 0.8813 (mm-30) cc_final: 0.8583 (mm-30) REVERT: C 67 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8874 (tm-30) REVERT: C 79 MET cc_start: 0.9070 (tpp) cc_final: 0.8693 (tpp) REVERT: C 88 ASP cc_start: 0.9228 (t70) cc_final: 0.8737 (t0) REVERT: C 91 GLU cc_start: 0.9182 (tm-30) cc_final: 0.8901 (tm-30) REVERT: C 96 GLU cc_start: 0.8869 (mm-30) cc_final: 0.8472 (mm-30) REVERT: C 113 GLU cc_start: 0.9252 (mp0) cc_final: 0.8872 (mp0) REVERT: C 125 GLU cc_start: 0.8473 (mm-30) cc_final: 0.8241 (tp30) REVERT: F 55 GLN cc_start: 0.7755 (mt0) cc_final: 0.7420 (mp10) REVERT: F 56 LYS cc_start: 0.8387 (tttt) cc_final: 0.8172 (mtpt) REVERT: E 60 LEU cc_start: 0.8887 (mt) cc_final: 0.8430 (mt) REVERT: E 97 GLU cc_start: 0.8640 (tt0) cc_final: 0.8095 (tt0) REVERT: H 27 GLN cc_start: 0.8926 (tm-30) cc_final: 0.8525 (tm-30) REVERT: H 91 LYS cc_start: 0.9179 (tttt) cc_final: 0.8697 (ttpt) REVERT: A 83 HIS cc_start: 0.8734 (m170) cc_final: 0.8202 (m170) REVERT: A 92 GLU cc_start: 0.9046 (tp30) cc_final: 0.8685 (tp30) REVERT: B 51 TYR cc_start: 0.9044 (t80) cc_final: 0.8711 (t80) REVERT: B 65 GLU cc_start: 0.8909 (tt0) cc_final: 0.8555 (tm-30) REVERT: K 229 MET cc_start: 0.8463 (mpp) cc_final: 0.7584 (mtt) REVERT: K 432 MET cc_start: 0.8996 (mmm) cc_final: 0.8405 (tpp) outliers start: 13 outliers final: 11 residues processed: 186 average time/residue: 0.2835 time to fit residues: 74.4537 Evaluate side-chains 181 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 170 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL 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 K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR 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 44 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 121 optimal weight: 0.6980 chunk 60 optimal weight: 4.9990 chunk 84 optimal weight: 7.9990 chunk 129 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 15 optimal weight: 0.0970 chunk 55 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.083794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3201 r_free = 0.3201 target = 0.056201 restraints weight = 54619.103| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.10 r_work: 0.2940 rms_B_bonded: 4.78 restraints_weight: 0.5000 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.6248 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= 0.167 Angle : 0.593 12.850 21168 Z= 0.323 Chirality : 0.034 0.240 2466 Planarity : 0.003 0.048 1798 Dihedral : 30.443 176.769 4014 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 1.84 % Allowed : 22.55 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.91 (0.25), residues: 1158 helix: 3.10 (0.18), residues: 769 sheet: 0.85 (0.61), residues: 69 loop : -0.94 (0.31), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 373 HIS 0.005 0.001 HIS H 75 PHE 0.015 0.001 PHE C 62 TYR 0.011 0.001 TYR D 57 ARG 0.004 0.000 ARG E 129 Details of bonding type rmsd hydrogen bonds : bond 0.04859 ( 663) hydrogen bonds : angle 3.30722 ( 1862) covalent geometry : bond 0.00375 (14830) covalent geometry : angle 0.59274 (21168) ********************** 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 180 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 88 ASP cc_start: 0.9099 (t0) cc_final: 0.8687 (t0) REVERT: D 96 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8541 (mm-30) REVERT: C 67 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8895 (tm-30) REVERT: C 79 MET cc_start: 0.9122 (tpp) cc_final: 0.8892 (tpp) REVERT: C 88 ASP cc_start: 0.9237 (t70) cc_final: 0.8771 (t0) REVERT: C 91 GLU cc_start: 0.9196 (tm-30) cc_final: 0.8935 (tm-30) REVERT: C 96 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8489 (mm-30) REVERT: C 113 GLU cc_start: 0.9267 (mp0) cc_final: 0.8918 (mp0) REVERT: C 125 GLU cc_start: 0.8545 (mm-30) cc_final: 0.8275 (tp30) REVERT: F 55 GLN cc_start: 0.7841 (mt0) cc_final: 0.7524 (mp10) REVERT: F 56 LYS cc_start: 0.8372 (tttt) cc_final: 0.8170 (mtpt) REVERT: E 60 LEU cc_start: 0.8886 (mt) cc_final: 0.8624 (mt) REVERT: E 97 GLU cc_start: 0.8699 (tt0) cc_final: 0.8115 (tt0) REVERT: H 27 GLN cc_start: 0.8953 (tm-30) cc_final: 0.8542 (tm-30) REVERT: H 91 LYS cc_start: 0.9208 (tttt) cc_final: 0.8739 (ttpt) REVERT: A 34 PHE cc_start: 0.9298 (m-80) cc_final: 0.9052 (m-80) REVERT: A 92 GLU cc_start: 0.9048 (tp30) cc_final: 0.8685 (tp30) REVERT: B 65 GLU cc_start: 0.8912 (tt0) cc_final: 0.8557 (tm-30) REVERT: K 229 MET cc_start: 0.8449 (mpp) cc_final: 0.7594 (mtt) REVERT: K 432 MET cc_start: 0.8983 (mmm) cc_final: 0.8408 (tpp) outliers start: 16 outliers final: 16 residues processed: 174 average time/residue: 0.2944 time to fit residues: 72.3095 Evaluate side-chains 178 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 76 SER Chi-restraints excluded: chain F residue 60 LEU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL 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 B residue 50 VAL Chi-restraints excluded: chain K residue 259 LEU Chi-restraints excluded: chain K residue 336 HIS Chi-restraints excluded: chain K residue 361 THR 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 98 optimal weight: 0.9980 chunk 107 optimal weight: 0.9980 chunk 34 optimal weight: 6.9990 chunk 69 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 83 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 105 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.083746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.055632 restraints weight = 57158.718| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 3.12 r_work: 0.2943 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.6357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 14830 Z= 0.159 Angle : 0.585 13.118 21168 Z= 0.319 Chirality : 0.034 0.230 2466 Planarity : 0.003 0.047 1798 Dihedral : 30.369 178.225 4014 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.19 % Allowed : 22.44 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.25), residues: 1158 helix: 3.12 (0.18), residues: 769 sheet: 0.70 (0.61), residues: 68 loop : -0.89 (0.31), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 373 HIS 0.004 0.001 HIS H 75 PHE 0.008 0.001 PHE E 104 TYR 0.010 0.001 TYR F 99 ARG 0.003 0.000 ARG E 72 Details of bonding type rmsd hydrogen bonds : bond 0.04695 ( 663) hydrogen bonds : angle 3.26519 ( 1862) covalent geometry : bond 0.00355 (14830) covalent geometry : angle 0.58493 (21168) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8016.58 seconds wall clock time: 138 minutes 43.00 seconds (8323.00 seconds total)