Starting phenix.real_space_refine on Sat Jun 14 21:17:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnv_61628/06_2025/9jnv_61628.cif" } resolution = 3.0 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= 0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 294 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 9707 2.51 5 N 3081 2.21 5 O 3728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 23 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16836 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 707 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 707 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 1, 'TRANS': 86} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} 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: "F" Number of atoms: 632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 632 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} 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: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4833 Classifications: {'peptide': 588} Link IDs: {'PCIS': 3, 'PTRANS': 18, 'TRANS': 566} Chain breaks: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.96, per 1000 atoms: 0.53 Number of scatterers: 16836 At special positions: 0 Unit cell: (97.425, 120.157, 156.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 294 15.00 Mg 1 11.99 O 3728 8.00 N 3081 7.00 C 9707 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.4 seconds 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2552 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 13 sheets defined 64.6% alpha, 3.6% beta 140 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.553A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.662A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.788A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.682A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.865A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 121 removed outlier: 3.831A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA D 121 " --> pdb=" O LYS D 117 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.184A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.897A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.585A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.648A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 removed outlier: 3.583A pdb=" N ILE F 34 " --> pdb=" O THR F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.777A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.502A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.723A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.670A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 88 removed outlier: 3.804A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 Processing helix chain 'K' and resid 119 through 130 removed outlier: 3.956A pdb=" N ILE K 123 " --> pdb=" O PHE K 119 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N SER K 125 " --> pdb=" O HIS K 121 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 143 removed outlier: 4.008A pdb=" N GLN K 135 " --> pdb=" O PRO K 131 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ASN K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 removed outlier: 3.542A pdb=" N ILE K 201 " --> pdb=" O ARG K 197 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 265 removed outlier: 3.761A pdb=" N LEU K 261 " --> pdb=" O LEU K 257 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 314 Processing helix chain 'K' and resid 325 through 329 Processing helix chain 'K' and resid 334 through 341 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.773A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) Processing helix chain 'K' and resid 378 through 386 Processing helix chain 'K' and resid 393 through 406 Processing helix chain 'K' and resid 413 through 417 Processing helix chain 'K' and resid 434 through 447 Processing helix chain 'K' and resid 467 through 476 removed outlier: 3.663A pdb=" N GLN K 471 " --> pdb=" O ASN K 467 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 482 Processing helix chain 'K' and resid 495 through 500 removed outlier: 4.394A pdb=" N ASN K 500 " --> pdb=" O HIS K 496 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 518 Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.577A pdb=" N LEU K 531 " --> pdb=" O MET K 527 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 579 through 583 removed outlier: 3.662A pdb=" N GLY K 582 " --> pdb=" O ARG K 579 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N LEU K 583 " --> pdb=" O ALA K 580 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 579 through 583' Processing helix chain 'K' and resid 601 through 614 removed outlier: 3.537A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ALA K 608 " --> pdb=" O ALA K 604 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N HIS K 613 " --> pdb=" O MET K 609 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 653 removed outlier: 4.153A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N GLN K 653 " --> pdb=" O LEU K 649 " (cutoff:3.500A) Processing helix chain 'K' and resid 707 through 728 removed outlier: 3.965A pdb=" N ASN K 717 " --> pdb=" O LEU K 713 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS K 718 " --> pdb=" O LYS K 714 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LYS K 720 " --> pdb=" O GLU K 716 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR K 728 " --> pdb=" O ALA K 724 " (cutoff:3.500A) Processing helix chain 'K' and resid 730 through 737 removed outlier: 4.119A pdb=" N PHE K 737 " --> pdb=" O ASP K 733 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.205A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.409A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.485A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.548A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.363A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.405A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU K 249 " --> pdb=" O ILE K 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'K' and resid 425 through 426 removed outlier: 6.698A pdb=" N LYS K 425 " --> pdb=" O VAL K 623 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'K' and resid 430 through 431 Processing sheet with id=AB4, first strand: chain 'K' and resid 521 through 525 removed outlier: 6.578A pdb=" N GLU K 544 " --> pdb=" O VAL K 573 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LEU K 575 " --> pdb=" O GLU K 544 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N CYS K 546 " --> pdb=" O LEU K 575 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N THR K 577 " --> pdb=" O CYS K 546 " (cutoff:3.500A) 593 hydrogen bonds defined for protein. 1737 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 7.40 Time building geometry restraints manager: 4.68 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 2280 1.32 - 1.44: 6077 1.44 - 1.56: 8750 1.56 - 1.68: 585 1.68 - 1.81: 43 Bond restraints: 17735 Sorted by residual: bond pdb=" CA LYS K 414 " pdb=" C LYS K 414 " ideal model delta sigma weight residual 1.522 1.409 0.113 1.40e-02 5.10e+03 6.50e+01 bond pdb=" CA THR K 419 " pdb=" C THR K 419 " ideal model delta sigma weight residual 1.523 1.456 0.067 1.34e-02 5.57e+03 2.53e+01 bond pdb=" CA PRO K 423 " pdb=" C PRO K 423 " ideal model delta sigma weight residual 1.521 1.461 0.060 1.20e-02 6.94e+03 2.52e+01 bond pdb=" CA LEU K 421 " pdb=" C LEU K 421 " ideal model delta sigma weight residual 1.528 1.471 0.057 1.18e-02 7.18e+03 2.31e+01 bond pdb=" N SER K 415 " pdb=" CA SER K 415 " ideal model delta sigma weight residual 1.462 1.404 0.058 1.36e-02 5.41e+03 1.84e+01 ... (remaining 17730 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.46: 24691 2.46 - 4.92: 459 4.92 - 7.38: 48 7.38 - 9.83: 4 9.83 - 12.29: 4 Bond angle restraints: 25206 Sorted by residual: angle pdb=" N LYS K 414 " pdb=" CA LYS K 414 " pdb=" C LYS K 414 " ideal model delta sigma weight residual 112.90 102.85 10.05 1.31e+00 5.83e-01 5.89e+01 angle pdb=" C PRO K 423 " pdb=" N LYS K 424 " pdb=" CA LYS K 424 " ideal model delta sigma weight residual 122.67 110.38 12.29 1.73e+00 3.34e-01 5.05e+01 angle pdb=" C VAL K 417 " pdb=" CA VAL K 417 " pdb=" CB VAL K 417 " ideal model delta sigma weight residual 111.06 106.27 4.79 8.80e-01 1.29e+00 2.96e+01 angle pdb=" N VAL K 417 " pdb=" CA VAL K 417 " pdb=" C VAL K 417 " ideal model delta sigma weight residual 112.96 107.76 5.20 1.00e+00 1.00e+00 2.71e+01 angle pdb=" C LYS K 414 " pdb=" N SER K 415 " pdb=" CA SER K 415 " ideal model delta sigma weight residual 122.31 114.59 7.72 1.81e+00 3.05e-01 1.82e+01 ... (remaining 25201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.63: 8332 33.63 - 67.27: 1581 67.27 - 100.90: 42 100.90 - 134.54: 1 134.54 - 168.17: 2 Dihedral angle restraints: 9958 sinusoidal: 6019 harmonic: 3939 Sorted by residual: dihedral pdb=" CA ARG B 23 " pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta harmonic sigma weight residual -180.00 -148.80 -31.20 0 5.00e+00 4.00e-02 3.89e+01 dihedral pdb=" C4' ADP K1202 " pdb=" C5' ADP K1202 " pdb=" O5' ADP K1202 " pdb=" PA ADP K1202 " ideal model delta sinusoidal sigma weight residual -180.00 -71.44 -108.56 1 2.00e+01 2.50e-03 3.16e+01 dihedral pdb=" C2' ADP K1202 " pdb=" C1' ADP K1202 " pdb=" N9 ADP K1202 " pdb=" C4 ADP K1202 " ideal model delta sinusoidal sigma weight residual 91.55 177.00 -85.45 1 2.00e+01 2.50e-03 2.21e+01 ... (remaining 9955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 2467 0.073 - 0.146: 372 0.146 - 0.219: 10 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 2850 Sorted by residual: chirality pdb=" CB ILE K 548 " pdb=" CA ILE K 548 " pdb=" CG1 ILE K 548 " pdb=" CG2 ILE K 548 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLU D 102 " pdb=" N GLU D 102 " pdb=" C GLU D 102 " pdb=" CB GLU D 102 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.88e-01 chirality pdb=" CA PRO D 47 " pdb=" N PRO D 47 " pdb=" C PRO D 47 " pdb=" CB PRO D 47 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.16e-01 ... (remaining 2847 not shown) Planarity restraints: 2187 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 413 " -0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C ILE K 413 " 0.080 2.00e-02 2.50e+03 pdb=" O ILE K 413 " -0.030 2.00e-02 2.50e+03 pdb=" N LYS K 414 " -0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 25 " -0.022 2.00e-02 2.50e+03 2.00e-02 6.99e+00 pdb=" CG PHE G 25 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 PHE G 25 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE G 25 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 25 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE G 25 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 100 " -0.035 2.00e-02 2.50e+03 1.50e-02 6.79e+00 pdb=" N9 DG I 100 " 0.034 2.00e-02 2.50e+03 pdb=" C8 DG I 100 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 100 " 0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 100 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 100 " -0.005 2.00e-02 2.50e+03 pdb=" O6 DG I 100 " -0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 100 " -0.007 2.00e-02 2.50e+03 pdb=" C2 DG I 100 " 0.006 2.00e-02 2.50e+03 pdb=" N2 DG I 100 " 0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 100 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DG I 100 " 0.000 2.00e-02 2.50e+03 ... (remaining 2184 not shown) Histogram of nonbonded interaction distances: 1.97 - 2.56: 177 2.56 - 3.14: 13824 3.14 - 3.73: 29218 3.73 - 4.31: 41005 4.31 - 4.90: 60325 Nonbonded interactions: 144549 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.969 2.170 nonbonded pdb=" N2 DG I 13 " pdb=" O2 DC J 135 " model vdw 2.103 2.496 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.106 3.040 nonbonded pdb=" OG1 THR D 87 " pdb=" OE1 GLU D 90 " model vdw 2.107 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.118 3.040 ... (remaining 144544 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 23 and (name N or name CA or name C or name O or name CB \ )) or resid 24 through 101)) selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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: 1.320 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: 42.230 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 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 : 0.012 0.113 17735 Z= 0.529 Angle : 0.869 12.293 25206 Z= 0.498 Chirality : 0.049 0.365 2850 Planarity : 0.004 0.046 2187 Dihedral : 25.745 168.172 7406 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.23 % Allowed : 7.94 % Favored : 91.84 % Rotamer: Outliers : 0.35 % Allowed : 0.86 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -0.62 (0.22), residues: 1323 helix: 0.72 (0.18), residues: 802 sheet: -2.47 (0.63), residues: 76 loop : -2.11 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP K 745 HIS 0.007 0.002 HIS F 75 PHE 0.046 0.003 PHE G 25 TYR 0.018 0.003 TYR K 596 ARG 0.008 0.001 ARG B 92 Details of bonding type rmsd hydrogen bonds : bond 0.13106 ( 951) hydrogen bonds : angle 5.11185 ( 2449) covalent geometry : bond 0.01165 (17735) covalent geometry : angle 0.86911 (25206) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 161 time to evaluate : 1.558 Fit side-chains revert: symmetry clash REVERT: C 92 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7247 (mt-10) REVERT: D 39 TYR cc_start: 0.8221 (t80) cc_final: 0.7919 (t80) REVERT: D 73 GLU cc_start: 0.7911 (tp30) cc_final: 0.7555 (tp30) REVERT: K 119 PHE cc_start: 0.8752 (m-80) cc_final: 0.8538 (m-80) outliers start: 4 outliers final: 1 residues processed: 165 average time/residue: 1.6028 time to fit residues: 288.7051 Evaluate side-chains 127 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 126 time to evaluate : 1.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 420 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 133 optimal weight: 4.9990 chunk 119 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 40 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 63 optimal weight: 0.2980 chunk 123 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 92 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 93 GLN F 93 GLN K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 620 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.093720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069056 restraints weight = 46682.304| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.21 r_work: 0.3123 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3123 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17735 Z= 0.166 Angle : 0.637 8.357 25206 Z= 0.355 Chirality : 0.037 0.153 2850 Planarity : 0.004 0.039 2187 Dihedral : 28.790 174.276 4685 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer: Outliers : 1.04 % Allowed : 10.46 % Favored : 88.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.61 (0.23), residues: 1323 helix: 1.70 (0.18), residues: 805 sheet: -1.84 (0.76), residues: 57 loop : -1.69 (0.27), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 600 HIS 0.008 0.001 HIS K 211 PHE 0.014 0.002 PHE G 25 TYR 0.014 0.001 TYR K 596 ARG 0.006 0.001 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.05098 ( 951) hydrogen bonds : angle 3.50231 ( 2449) covalent geometry : bond 0.00357 (17735) covalent geometry : angle 0.63723 (25206) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 179 time to evaluate : 1.416 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8309 (mm-30) REVERT: C 92 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 39 TYR cc_start: 0.8444 (t80) cc_final: 0.7974 (t80) REVERT: E 97 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8033 (mp0) REVERT: H 39 TYR cc_start: 0.8272 (t80) cc_final: 0.8052 (t80) REVERT: H 54 LYS cc_start: 0.9153 (mmpt) cc_final: 0.8811 (mmtt) REVERT: H 90 GLU cc_start: 0.8893 (mp0) cc_final: 0.8510 (mp0) REVERT: K 119 PHE cc_start: 0.8723 (m-80) cc_final: 0.8515 (m-80) REVERT: K 735 GLN cc_start: 0.8780 (pt0) cc_final: 0.8234 (pt0) outliers start: 12 outliers final: 4 residues processed: 183 average time/residue: 1.5757 time to fit residues: 316.5368 Evaluate side-chains 143 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 137 time to evaluate : 1.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 94 optimal weight: 5.9990 chunk 136 optimal weight: 0.0970 chunk 133 optimal weight: 9.9990 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 0.0970 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 9.9990 chunk 37 optimal weight: 0.3980 chunk 139 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.094694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.069995 restraints weight = 46557.648| |-----------------------------------------------------------------------------| r_work (start): 0.3294 rms_B_bonded: 2.21 r_work: 0.3144 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3144 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17735 Z= 0.149 Angle : 0.587 9.016 25206 Z= 0.330 Chirality : 0.036 0.238 2850 Planarity : 0.004 0.037 2187 Dihedral : 28.486 176.110 4684 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.64 % Allowed : 15.13 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.02 (0.24), residues: 1323 helix: 2.03 (0.18), residues: 809 sheet: -1.58 (0.77), residues: 57 loop : -1.58 (0.28), residues: 457 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 267 HIS 0.011 0.001 HIS K 211 PHE 0.011 0.001 PHE K 234 TYR 0.015 0.001 TYR K 320 ARG 0.005 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04590 ( 951) hydrogen bonds : angle 3.22789 ( 2449) covalent geometry : bond 0.00322 (17735) covalent geometry : angle 0.58713 (25206) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8477 (pm20) cc_final: 0.8207 (pm20) REVERT: A 79 LYS cc_start: 0.8540 (tttp) cc_final: 0.8184 (mtpt) REVERT: A 94 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8291 (mm-30) REVERT: B 74 GLU cc_start: 0.8096 (tp30) cc_final: 0.7893 (tp30) REVERT: C 15 LYS cc_start: 0.8390 (ttpm) cc_final: 0.7971 (ttpp) REVERT: C 61 GLU cc_start: 0.8100 (tp30) cc_final: 0.7859 (tp30) REVERT: C 92 GLU cc_start: 0.8178 (mt-10) cc_final: 0.7625 (mt-10) REVERT: D 39 TYR cc_start: 0.8450 (t80) cc_final: 0.8001 (t80) REVERT: E 97 GLU cc_start: 0.8388 (OUTLIER) cc_final: 0.8018 (mp0) REVERT: G 13 LYS cc_start: 0.9148 (tptt) cc_final: 0.8764 (mmmm) REVERT: G 90 ASP cc_start: 0.8762 (t70) cc_final: 0.8534 (t70) REVERT: H 39 TYR cc_start: 0.8289 (t80) cc_final: 0.8043 (t80) REVERT: H 54 LYS cc_start: 0.9166 (mmpt) cc_final: 0.8821 (mmtt) REVERT: H 56 MET cc_start: 0.9181 (tpp) cc_final: 0.8904 (tpt) REVERT: H 65 ASP cc_start: 0.8962 (t0) cc_final: 0.8725 (t0) REVERT: H 90 GLU cc_start: 0.8900 (mp0) cc_final: 0.8511 (mp0) REVERT: K 510 LEU cc_start: 0.9448 (tm) cc_final: 0.9153 (pp) REVERT: K 735 GLN cc_start: 0.8769 (pt0) cc_final: 0.8332 (pt0) outliers start: 19 outliers final: 6 residues processed: 183 average time/residue: 1.5640 time to fit residues: 313.3587 Evaluate side-chains 155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 147 time to evaluate : 1.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 475 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 60 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 120 optimal weight: 0.5980 chunk 130 optimal weight: 3.9990 chunk 50 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 81 ASN K 81 HIS ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 748 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.095013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.070235 restraints weight = 46887.773| |-----------------------------------------------------------------------------| r_work (start): 0.3299 rms_B_bonded: 2.23 r_work: 0.3148 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3148 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 17735 Z= 0.152 Angle : 0.579 9.692 25206 Z= 0.326 Chirality : 0.035 0.250 2850 Planarity : 0.003 0.033 2187 Dihedral : 28.336 176.746 4684 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.64 % Allowed : 17.37 % Favored : 80.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.18 (0.24), residues: 1323 helix: 2.12 (0.18), residues: 814 sheet: -1.75 (0.71), residues: 64 loop : -1.44 (0.28), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 267 HIS 0.011 0.001 HIS K 211 PHE 0.010 0.001 PHE K 234 TYR 0.012 0.001 TYR K 596 ARG 0.004 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04474 ( 951) hydrogen bonds : angle 3.13120 ( 2449) covalent geometry : bond 0.00336 (17735) covalent geometry : angle 0.57862 (25206) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.360 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8470 (pm20) cc_final: 0.8175 (pm20) REVERT: A 73 GLU cc_start: 0.9043 (tt0) cc_final: 0.8813 (tt0) REVERT: A 90 MET cc_start: 0.9033 (OUTLIER) cc_final: 0.8823 (mmm) REVERT: A 94 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8304 (mm-30) REVERT: B 74 GLU cc_start: 0.8100 (tp30) cc_final: 0.7774 (mm-30) REVERT: C 15 LYS cc_start: 0.8260 (ttpm) cc_final: 0.7971 (ttpp) REVERT: C 92 GLU cc_start: 0.8148 (mt-10) cc_final: 0.7602 (mt-10) REVERT: D 39 TYR cc_start: 0.8425 (t80) cc_final: 0.8006 (t80) REVERT: E 97 GLU cc_start: 0.8414 (OUTLIER) cc_final: 0.7995 (mp0) REVERT: F 93 GLN cc_start: 0.8583 (OUTLIER) cc_final: 0.7827 (mp10) REVERT: G 13 LYS cc_start: 0.9133 (tptt) cc_final: 0.8737 (mmmm) REVERT: G 90 ASP cc_start: 0.8663 (t70) cc_final: 0.8226 (t70) REVERT: G 92 GLU cc_start: 0.8828 (mp0) cc_final: 0.8434 (pm20) REVERT: H 39 TYR cc_start: 0.8287 (t80) cc_final: 0.8019 (t80) REVERT: H 54 LYS cc_start: 0.9176 (mmpt) cc_final: 0.8821 (mmtt) REVERT: H 56 MET cc_start: 0.9205 (tpp) cc_final: 0.8945 (tpt) REVERT: H 65 ASP cc_start: 0.8951 (t0) cc_final: 0.8610 (t0) REVERT: H 90 GLU cc_start: 0.8909 (mp0) cc_final: 0.8493 (mp0) REVERT: K 510 LEU cc_start: 0.9514 (tm) cc_final: 0.9209 (pp) outliers start: 19 outliers final: 7 residues processed: 167 average time/residue: 1.5048 time to fit residues: 274.8988 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 148 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain K residue 333 GLU Chi-restraints excluded: chain K residue 347 ASN Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 475 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 115 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 107 optimal weight: 9.9990 chunk 61 optimal weight: 0.5980 chunk 135 optimal weight: 0.0870 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 52 optimal weight: 0.6980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 HIS ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.096029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.071699 restraints weight = 47337.817| |-----------------------------------------------------------------------------| r_work (start): 0.3337 rms_B_bonded: 2.21 r_work: 0.3190 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17735 Z= 0.139 Angle : 0.569 11.050 25206 Z= 0.320 Chirality : 0.035 0.194 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.159 177.239 4684 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.82 % Allowed : 18.93 % Favored : 79.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.35 (0.24), residues: 1323 helix: 2.26 (0.18), residues: 807 sheet: -1.69 (0.70), residues: 64 loop : -1.31 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 267 HIS 0.012 0.001 HIS K 211 PHE 0.011 0.001 PHE K 234 TYR 0.011 0.001 TYR K 320 ARG 0.005 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 951) hydrogen bonds : angle 3.04100 ( 2449) covalent geometry : bond 0.00302 (17735) covalent geometry : angle 0.56911 (25206) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 1.591 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8424 (pm20) cc_final: 0.8042 (pm20) REVERT: A 90 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8759 (mmm) REVERT: A 94 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: B 74 GLU cc_start: 0.7886 (tp30) cc_final: 0.7676 (mm-30) REVERT: C 15 LYS cc_start: 0.8197 (ttpm) cc_final: 0.7725 (ttpm) REVERT: C 92 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7554 (mt-10) REVERT: D 39 TYR cc_start: 0.8427 (t80) cc_final: 0.8009 (t80) REVERT: E 97 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: F 93 GLN cc_start: 0.8514 (OUTLIER) cc_final: 0.7658 (mp10) REVERT: G 13 LYS cc_start: 0.9121 (tptt) cc_final: 0.8710 (mmmm) REVERT: H 39 TYR cc_start: 0.8334 (t80) cc_final: 0.8059 (t80) REVERT: H 54 LYS cc_start: 0.9105 (mmpt) cc_final: 0.8696 (mmtt) REVERT: H 65 ASP cc_start: 0.8976 (t0) cc_final: 0.8681 (t0) REVERT: H 90 GLU cc_start: 0.8835 (mp0) cc_final: 0.8448 (mp0) REVERT: K 333 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7517 (tm-30) REVERT: K 510 LEU cc_start: 0.9488 (tm) cc_final: 0.9206 (pp) outliers start: 21 outliers final: 4 residues processed: 166 average time/residue: 1.5531 time to fit residues: 282.2505 Evaluate side-chains 151 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 142 time to evaluate : 1.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 333 GLU Chi-restraints excluded: chain K residue 390 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 66 optimal weight: 2.9990 chunk 124 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 107 optimal weight: 10.0000 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 116 optimal weight: 6.9990 chunk 44 optimal weight: 0.8980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 81 HIS ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070087 restraints weight = 47243.797| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.22 r_work: 0.3152 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8444 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17735 Z= 0.176 Angle : 0.593 11.683 25206 Z= 0.331 Chirality : 0.035 0.152 2850 Planarity : 0.004 0.030 2187 Dihedral : 28.248 176.551 4684 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 19.79 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.34 (0.24), residues: 1323 helix: 2.24 (0.18), residues: 810 sheet: -1.72 (0.71), residues: 64 loop : -1.31 (0.29), residues: 449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 267 HIS 0.013 0.001 HIS K 211 PHE 0.014 0.001 PHE K 234 TYR 0.014 0.001 TYR K 596 ARG 0.007 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04784 ( 951) hydrogen bonds : angle 3.12383 ( 2449) covalent geometry : bond 0.00393 (17735) covalent geometry : angle 0.59296 (25206) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 148 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 90 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8792 (mmm) REVERT: A 94 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: B 74 GLU cc_start: 0.8009 (tp30) cc_final: 0.7788 (mm-30) REVERT: C 15 LYS cc_start: 0.8245 (ttpm) cc_final: 0.7995 (ttpp) REVERT: C 92 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7788 (mt-10) REVERT: D 39 TYR cc_start: 0.8489 (t80) cc_final: 0.8070 (t80) REVERT: E 97 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: F 93 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7852 (mp10) REVERT: G 13 LYS cc_start: 0.9160 (tptt) cc_final: 0.8743 (mmmm) REVERT: H 39 TYR cc_start: 0.8339 (t80) cc_final: 0.8061 (t80) REVERT: H 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8672 (t0) REVERT: H 90 GLU cc_start: 0.8906 (mp0) cc_final: 0.8497 (mp0) REVERT: K 510 LEU cc_start: 0.9511 (tm) cc_final: 0.9205 (pp) outliers start: 23 outliers final: 11 residues processed: 159 average time/residue: 1.7901 time to fit residues: 311.5399 Evaluate side-chains 154 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 90 MET Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 333 GLU Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 596 TYR Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 87 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 155 optimal weight: 6.9990 chunk 40 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 102 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.094207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.069428 restraints weight = 46892.120| |-----------------------------------------------------------------------------| r_work (start): 0.3287 rms_B_bonded: 2.21 r_work: 0.3136 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17735 Z= 0.196 Angle : 0.607 12.230 25206 Z= 0.338 Chirality : 0.036 0.150 2850 Planarity : 0.004 0.030 2187 Dihedral : 28.315 176.404 4684 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 2.59 % Allowed : 19.45 % Favored : 77.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.32 (0.24), residues: 1323 helix: 2.23 (0.18), residues: 804 sheet: -1.72 (0.72), residues: 64 loop : -1.27 (0.28), residues: 455 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 267 HIS 0.013 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.014 0.001 TYR K 596 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04968 ( 951) hydrogen bonds : angle 3.17078 ( 2449) covalent geometry : bond 0.00442 (17735) covalent geometry : angle 0.60735 (25206) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 148 time to evaluate : 1.353 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8523 (pm20) cc_final: 0.8245 (pm20) REVERT: A 94 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8346 (mm-30) REVERT: A 120 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8495 (mtm) REVERT: B 74 GLU cc_start: 0.8066 (tp30) cc_final: 0.7834 (mm-30) REVERT: C 15 LYS cc_start: 0.8287 (ttpm) cc_final: 0.7963 (ttpt) REVERT: C 92 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7844 (mt-10) REVERT: D 39 TYR cc_start: 0.8485 (t80) cc_final: 0.8034 (t80) REVERT: E 97 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: F 93 GLN cc_start: 0.8663 (OUTLIER) cc_final: 0.7878 (mp10) REVERT: G 13 LYS cc_start: 0.9160 (tptt) cc_final: 0.8746 (mmmm) REVERT: H 39 TYR cc_start: 0.8352 (t80) cc_final: 0.8075 (t80) REVERT: H 65 ASP cc_start: 0.8943 (t0) cc_final: 0.8687 (t0) REVERT: H 90 GLU cc_start: 0.8922 (mp0) cc_final: 0.8500 (mp0) REVERT: K 333 GLU cc_start: 0.8257 (mp0) cc_final: 0.7578 (tm-30) REVERT: K 510 LEU cc_start: 0.9517 (tm) cc_final: 0.9210 (pp) outliers start: 30 outliers final: 11 residues processed: 165 average time/residue: 1.6580 time to fit residues: 299.3229 Evaluate side-chains 157 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 500 ASN Chi-restraints excluded: chain K residue 596 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 80 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 chunk 137 optimal weight: 4.9990 chunk 152 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 157 optimal weight: 9.9990 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 3.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.094779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.070132 restraints weight = 46741.338| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.19 r_work: 0.3152 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17735 Z= 0.171 Angle : 0.609 12.403 25206 Z= 0.336 Chirality : 0.035 0.165 2850 Planarity : 0.004 0.029 2187 Dihedral : 28.278 176.859 4684 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.82 % Allowed : 21.09 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.33 (0.24), residues: 1323 helix: 2.20 (0.18), residues: 812 sheet: -1.67 (0.72), residues: 64 loop : -1.26 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 267 HIS 0.014 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.013 0.001 TYR K 596 ARG 0.006 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04669 ( 951) hydrogen bonds : angle 3.09616 ( 2449) covalent geometry : bond 0.00382 (17735) covalent geometry : angle 0.60930 (25206) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 151 time to evaluate : 1.544 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8460 (pm20) cc_final: 0.8178 (pm20) REVERT: A 94 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8300 (mm-30) REVERT: A 120 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8492 (mtm) REVERT: B 53 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7396 (mm-30) REVERT: B 74 GLU cc_start: 0.8005 (tp30) cc_final: 0.7779 (mm-30) REVERT: C 15 LYS cc_start: 0.8277 (ttpm) cc_final: 0.7959 (ttpt) REVERT: C 92 GLU cc_start: 0.8207 (mt-10) cc_final: 0.7790 (mt-10) REVERT: D 39 TYR cc_start: 0.8472 (t80) cc_final: 0.8038 (t80) REVERT: E 97 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: F 93 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.7861 (mp10) REVERT: G 13 LYS cc_start: 0.9111 (tptt) cc_final: 0.8728 (mmmm) REVERT: H 39 TYR cc_start: 0.8344 (t80) cc_final: 0.8058 (t80) REVERT: H 56 MET cc_start: 0.9189 (tpp) cc_final: 0.8925 (tpt) REVERT: H 65 ASP cc_start: 0.8942 (t0) cc_final: 0.8675 (t0) REVERT: H 90 GLU cc_start: 0.8897 (mp0) cc_final: 0.8493 (mp0) REVERT: K 333 GLU cc_start: 0.8331 (mp0) cc_final: 0.7637 (tm-30) REVERT: K 510 LEU cc_start: 0.9495 (tm) cc_final: 0.9197 (pp) REVERT: K 735 GLN cc_start: 0.9213 (tt0) cc_final: 0.8841 (pt0) outliers start: 21 outliers final: 10 residues processed: 161 average time/residue: 1.6314 time to fit residues: 287.3405 Evaluate side-chains 161 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 146 time to evaluate : 1.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 211 HIS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 475 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 32 optimal weight: 1.9990 chunk 143 optimal weight: 1.9990 chunk 156 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.094663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.070075 restraints weight = 47158.209| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.20 r_work: 0.3151 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.2592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17735 Z= 0.172 Angle : 0.611 12.907 25206 Z= 0.338 Chirality : 0.036 0.330 2850 Planarity : 0.004 0.029 2187 Dihedral : 28.266 177.008 4684 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.90 % Allowed : 21.61 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.31 (0.24), residues: 1323 helix: 2.16 (0.18), residues: 812 sheet: -1.65 (0.73), residues: 64 loop : -1.23 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 267 HIS 0.023 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.014 0.001 TYR K 596 ARG 0.006 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04710 ( 951) hydrogen bonds : angle 3.13459 ( 2449) covalent geometry : bond 0.00386 (17735) covalent geometry : angle 0.61133 (25206) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 148 time to evaluate : 1.500 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8481 (pm20) cc_final: 0.8230 (pm20) REVERT: A 94 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8292 (mm-30) REVERT: A 120 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8488 (mtm) REVERT: C 15 LYS cc_start: 0.8279 (ttpm) cc_final: 0.7958 (ttpt) REVERT: C 92 GLU cc_start: 0.8117 (mt-10) cc_final: 0.7792 (mt-10) REVERT: D 39 TYR cc_start: 0.8501 (t80) cc_final: 0.8045 (t80) REVERT: E 97 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7958 (mp0) REVERT: F 93 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7836 (mp10) REVERT: G 13 LYS cc_start: 0.9143 (tptt) cc_final: 0.8759 (mmmm) REVERT: H 39 TYR cc_start: 0.8338 (t80) cc_final: 0.8049 (t80) REVERT: H 56 MET cc_start: 0.9190 (tpp) cc_final: 0.8924 (tpt) REVERT: H 65 ASP cc_start: 0.8946 (t0) cc_final: 0.8683 (t0) REVERT: H 90 GLU cc_start: 0.8871 (mp0) cc_final: 0.8461 (mp0) REVERT: K 510 LEU cc_start: 0.9483 (tm) cc_final: 0.9198 (pp) REVERT: K 735 GLN cc_start: 0.9205 (tt0) cc_final: 0.8850 (pt0) outliers start: 22 outliers final: 13 residues processed: 158 average time/residue: 1.5839 time to fit residues: 273.6764 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 146 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 333 GLU Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 594 VAL Chi-restraints excluded: chain K residue 596 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 135 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 151 optimal weight: 0.7980 chunk 155 optimal weight: 6.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.095003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.070364 restraints weight = 47149.681| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.21 r_work: 0.3157 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.2657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 17735 Z= 0.167 Angle : 0.620 13.072 25206 Z= 0.340 Chirality : 0.036 0.297 2850 Planarity : 0.004 0.029 2187 Dihedral : 28.238 177.177 4684 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.47 % Allowed : 22.04 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.33 (0.24), residues: 1323 helix: 2.16 (0.18), residues: 816 sheet: -1.63 (0.73), residues: 64 loop : -1.23 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 267 HIS 0.014 0.001 HIS K 211 PHE 0.016 0.001 PHE K 234 TYR 0.013 0.001 TYR K 596 ARG 0.005 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04627 ( 951) hydrogen bonds : angle 3.11417 ( 2449) covalent geometry : bond 0.00373 (17735) covalent geometry : angle 0.62023 (25206) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2646 Ramachandran restraints generated. 1323 Oldfield, 0 Emsley, 1323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.573 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8487 (pm20) cc_final: 0.8196 (pm20) REVERT: A 94 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8284 (mm-30) REVERT: A 120 MET cc_start: 0.8990 (OUTLIER) cc_final: 0.8485 (mtm) REVERT: C 15 LYS cc_start: 0.8288 (ttpm) cc_final: 0.7975 (ttpt) REVERT: C 92 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7872 (mt-10) REVERT: D 39 TYR cc_start: 0.8465 (t80) cc_final: 0.8018 (t80) REVERT: E 97 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7950 (mp0) REVERT: F 93 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7828 (mp10) REVERT: G 13 LYS cc_start: 0.9141 (tptt) cc_final: 0.8751 (mmmm) REVERT: H 39 TYR cc_start: 0.8338 (t80) cc_final: 0.8047 (t80) REVERT: H 56 MET cc_start: 0.9187 (tpp) cc_final: 0.8926 (tpt) REVERT: H 65 ASP cc_start: 0.8947 (t0) cc_final: 0.8675 (t0) REVERT: H 90 GLU cc_start: 0.8894 (mp0) cc_final: 0.8498 (mp0) REVERT: K 93 LYS cc_start: 0.8384 (mptt) cc_final: 0.8086 (mmtt) REVERT: K 333 GLU cc_start: 0.8319 (mp0) cc_final: 0.7681 (tm-30) REVERT: K 385 PHE cc_start: 0.7546 (t80) cc_final: 0.7221 (t80) REVERT: K 510 LEU cc_start: 0.9483 (tm) cc_final: 0.9170 (pp) REVERT: K 735 GLN cc_start: 0.9228 (tt0) cc_final: 0.8692 (mt0) outliers start: 17 outliers final: 12 residues processed: 160 average time/residue: 1.6839 time to fit residues: 295.4271 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 93 GLN Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 29 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 211 HIS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 594 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 0.6980 chunk 119 optimal weight: 0.6980 chunk 50 optimal weight: 0.2980 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 126 optimal weight: 0.9980 chunk 56 optimal weight: 0.0070 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 211 HIS ** K 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.096402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.072133 restraints weight = 46996.092| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.20 r_work: 0.3195 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.2913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17735 Z= 0.140 Angle : 0.600 13.080 25206 Z= 0.331 Chirality : 0.035 0.255 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.082 178.035 4684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.56 % Allowed : 22.21 % Favored : 76.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.82 % 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: 1.41 (0.24), residues: 1323 helix: 2.21 (0.18), residues: 816 sheet: -1.53 (0.73), residues: 64 loop : -1.17 (0.29), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 267 HIS 0.007 0.001 HIS K 211 PHE 0.014 0.001 PHE K 234 TYR 0.012 0.001 TYR K 596 ARG 0.005 0.000 ARG H 76 Details of bonding type rmsd hydrogen bonds : bond 0.04184 ( 951) hydrogen bonds : angle 3.03439 ( 2449) covalent geometry : bond 0.00305 (17735) covalent geometry : angle 0.59970 (25206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10066.64 seconds wall clock time: 174 minutes 40.58 seconds (10480.58 seconds total)