Starting phenix.real_space_refine on Sun May 18 04:54:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnv_61628/05_2025/9jnv_61628.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnv_61628/05_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_61628/05_2025/9jnv_61628.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnv_61628/05_2025/9jnv_61628.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnv_61628/05_2025/9jnv_61628.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnv_61628/05_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-5687/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: 9.18, per 1000 atoms: 0.55 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: 4.25 Conformation dependent library (CDL) restraints added in 1.5 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: 6.98 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: 7.84 Time building geometry restraints manager: 4.95 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: 3.520 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: 0.000 Extract box with map and model: 2.820 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 41.010 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: 0.010 Load rotamer database and sin/cos tables:10.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.890 ------------------------------------------------------------------------------- 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 : 1.545 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: 1.6485 time to fit residues: 296.6572 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 : 1.319 ------------------------------------------------------------------------------- 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 = 42)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069050 restraints weight = 46682.286| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 2.21 r_work: 0.3122 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- 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 : 1.458 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8310 (mm-30) REVERT: C 92 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 39 TYR cc_start: 0.8445 (t80) cc_final: 0.7975 (t80) REVERT: E 97 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.8034 (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: 0.8727 (m-80) cc_final: 0.8516 (m-80) REVERT: K 735 GLN cc_start: 0.8779 (pt0) cc_final: 0.8233 (pt0) outliers start: 12 outliers final: 4 residues processed: 183 average time/residue: 1.4584 time to fit residues: 293.7171 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 : 1.630 ------------------------------------------------------------------------------- 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: 0.4980 chunk 133 optimal weight: 10.0000 chunk 84 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 54 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 107 optimal weight: 8.9990 chunk 37 optimal weight: 0.4980 chunk 139 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.3782 r_free = 0.3782 target = 0.093905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.069095 restraints weight = 46521.223| |-----------------------------------------------------------------------------| r_work (start): 0.3274 rms_B_bonded: 2.22 r_work: 0.3122 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.1928 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= 0.165 Angle : 0.597 8.951 25206 Z= 0.335 Chirality : 0.036 0.243 2850 Planarity : 0.004 0.035 2187 Dihedral : 28.578 175.575 4684 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.38 % Allowed : 15.21 % Favored : 83.41 % 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: 0.96 (0.24), residues: 1323 helix: 1.98 (0.18), residues: 808 sheet: -1.62 (0.77), residues: 57 loop : -1.59 (0.28), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 267 HIS 0.010 0.001 HIS K 211 PHE 0.012 0.001 PHE G 25 TYR 0.013 0.001 TYR K 320 ARG 0.005 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04875 ( 951) hydrogen bonds : angle 3.29685 ( 2449) covalent geometry : bond 0.00363 (17735) covalent geometry : angle 0.59713 (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 181 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 1.496 Fit side-chains revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8999 (tt0) cc_final: 0.8781 (tt0) REVERT: A 94 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8313 (mm-30) REVERT: B 74 GLU cc_start: 0.8186 (tp30) cc_final: 0.7954 (tp30) REVERT: C 15 LYS cc_start: 0.8413 (ttpm) cc_final: 0.7993 (ttpp) REVERT: C 92 GLU cc_start: 0.8194 (mt-10) cc_final: 0.7615 (mt-10) REVERT: D 39 TYR cc_start: 0.8478 (t80) cc_final: 0.8018 (t80) REVERT: D 76 ARG cc_start: 0.8555 (mtp180) cc_final: 0.8338 (mtm-85) REVERT: E 97 GLU cc_start: 0.8415 (OUTLIER) cc_final: 0.8002 (mp0) REVERT: H 39 TYR cc_start: 0.8291 (t80) cc_final: 0.8083 (t80) REVERT: H 54 LYS cc_start: 0.9167 (mmpt) cc_final: 0.8824 (mmtt) REVERT: H 65 ASP cc_start: 0.8976 (t0) cc_final: 0.8718 (t0) REVERT: H 90 GLU cc_start: 0.8922 (mp0) cc_final: 0.8517 (mp0) REVERT: K 510 LEU cc_start: 0.9446 (tm) cc_final: 0.9160 (pp) REVERT: K 735 GLN cc_start: 0.8731 (pt0) cc_final: 0.8293 (pt0) outliers start: 16 outliers final: 6 residues processed: 173 average time/residue: 1.5292 time to fit residues: 290.0335 Evaluate side-chains 148 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 140 time to evaluate : 1.389 ------------------------------------------------------------------------------- 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: 3.9990 chunk 120 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 156 optimal weight: 10.0000 chunk 14 optimal weight: 0.8980 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 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 = 0.3782 r_free = 0.3782 target = 0.093892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.068921 restraints weight = 46951.235| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.23 r_work: 0.3117 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 17735 Z= 0.179 Angle : 0.591 9.613 25206 Z= 0.332 Chirality : 0.036 0.272 2850 Planarity : 0.004 0.030 2187 Dihedral : 28.480 176.155 4684 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 2.16 % Allowed : 16.94 % Favored : 80.90 % 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: 1.07 (0.24), residues: 1323 helix: 2.04 (0.18), residues: 812 sheet: -1.80 (0.71), residues: 64 loop : -1.47 (0.28), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 267 HIS 0.011 0.001 HIS K 211 PHE 0.012 0.002 PHE G 25 TYR 0.013 0.001 TYR K 596 ARG 0.004 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04895 ( 951) hydrogen bonds : angle 3.22549 ( 2449) covalent geometry : bond 0.00401 (17735) covalent geometry : angle 0.59131 (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 182 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 157 time to evaluate : 1.370 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8341 (mm-30) REVERT: B 74 GLU cc_start: 0.8136 (tp30) cc_final: 0.7898 (mm-30) REVERT: C 15 LYS cc_start: 0.8355 (ttpm) cc_final: 0.8148 (ttpp) REVERT: C 92 GLU cc_start: 0.8190 (mt-10) cc_final: 0.7540 (mt-10) REVERT: D 39 TYR cc_start: 0.8466 (t80) cc_final: 0.8003 (t80) REVERT: D 76 ARG cc_start: 0.8587 (mtp180) cc_final: 0.8377 (mtm-85) REVERT: E 97 GLU cc_start: 0.8440 (OUTLIER) cc_final: 0.8046 (mp0) REVERT: F 93 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7860 (mp10) REVERT: H 39 TYR cc_start: 0.8293 (t80) cc_final: 0.8065 (t80) REVERT: H 54 LYS cc_start: 0.9214 (mmpt) cc_final: 0.8859 (mmtt) REVERT: H 65 ASP cc_start: 0.8937 (t0) cc_final: 0.8612 (t0) REVERT: H 90 GLU cc_start: 0.8930 (mp0) cc_final: 0.8493 (mp0) REVERT: K 132 LYS cc_start: 0.9422 (tppt) cc_final: 0.9151 (OUTLIER) REVERT: K 510 LEU cc_start: 0.9469 (tm) cc_final: 0.9179 (pp) outliers start: 25 outliers final: 14 residues processed: 170 average time/residue: 1.4442 time to fit residues: 270.1288 Evaluate side-chains 162 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 D residue 87 THR 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 H residue 115 VAL 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: 5.9990 chunk 123 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 51 optimal weight: 0.8980 chunk 107 optimal weight: 7.9990 chunk 61 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 45 optimal weight: 0.2980 chunk 69 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.095549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.071095 restraints weight = 47465.362| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.22 r_work: 0.3173 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3173 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2470 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= 0.141 Angle : 0.580 10.587 25206 Z= 0.324 Chirality : 0.035 0.209 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.265 177.146 4684 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.64 % Allowed : 19.10 % 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: 1.28 (0.24), residues: 1323 helix: 2.22 (0.18), residues: 808 sheet: -1.75 (0.71), residues: 64 loop : -1.38 (0.28), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 267 HIS 0.012 0.001 HIS K 211 PHE 0.017 0.001 PHE K 119 TYR 0.012 0.001 TYR K 320 ARG 0.005 0.000 ARG K 611 Details of bonding type rmsd hydrogen bonds : bond 0.04290 ( 951) hydrogen bonds : angle 3.07776 ( 2449) covalent geometry : bond 0.00306 (17735) covalent geometry : angle 0.58015 (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 178 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 159 time to evaluate : 1.429 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8946 (mt-10) cc_final: 0.8736 (mt-10) REVERT: A 59 GLU cc_start: 0.8509 (pm20) cc_final: 0.8218 (pm20) REVERT: A 90 MET cc_start: 0.9016 (mpp) cc_final: 0.8815 (mmm) REVERT: A 94 GLU cc_start: 0.8525 (OUTLIER) cc_final: 0.8262 (mm-30) REVERT: C 15 LYS cc_start: 0.8235 (ttpm) cc_final: 0.7752 (ttpm) REVERT: C 92 GLU cc_start: 0.8220 (mt-10) cc_final: 0.7527 (mt-10) REVERT: D 39 TYR cc_start: 0.8417 (t80) cc_final: 0.8022 (t80) REVERT: D 76 ARG cc_start: 0.8588 (mtp180) cc_final: 0.8376 (mtm-85) REVERT: E 97 GLU cc_start: 0.8419 (OUTLIER) cc_final: 0.8039 (mp0) REVERT: F 93 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.7727 (mp10) REVERT: G 90 ASP cc_start: 0.8607 (t0) cc_final: 0.8346 (t0) REVERT: H 39 TYR cc_start: 0.8314 (t80) cc_final: 0.8046 (t80) REVERT: H 54 LYS cc_start: 0.9109 (mmpt) cc_final: 0.8696 (mmtt) REVERT: H 65 ASP cc_start: 0.8944 (t0) cc_final: 0.8679 (t0) REVERT: H 90 GLU cc_start: 0.8842 (mp0) cc_final: 0.8452 (mp0) REVERT: K 134 ARG cc_start: 0.9257 (mmm160) cc_final: 0.9003 (mmm160) REVERT: K 333 GLU cc_start: 0.8263 (mp0) cc_final: 0.7548 (tm-30) REVERT: K 510 LEU cc_start: 0.9421 (tm) cc_final: 0.9156 (pp) outliers start: 19 outliers final: 3 residues processed: 167 average time/residue: 1.4568 time to fit residues: 266.9970 Evaluate side-chains 149 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 143 time to evaluate : 1.349 ------------------------------------------------------------------------------- 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 F residue 93 GLN 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: 5.9990 chunk 6 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 116 optimal weight: 4.9990 chunk 44 optimal weight: 0.4980 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 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3793 r_free = 0.3793 target = 0.094517 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069712 restraints weight = 46822.082| |-----------------------------------------------------------------------------| r_work (start): 0.3286 rms_B_bonded: 2.21 r_work: 0.3136 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2449 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= 0.172 Angle : 0.593 11.666 25206 Z= 0.330 Chirality : 0.035 0.182 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.295 176.640 4684 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 1.73 % Allowed : 20.05 % 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: 1.31 (0.24), residues: 1323 helix: 2.20 (0.18), residues: 814 sheet: -1.45 (0.66), residues: 78 loop : -1.37 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 267 HIS 0.012 0.001 HIS K 211 PHE 0.013 0.001 PHE K 234 TYR 0.013 0.001 TYR K 596 ARG 0.004 0.000 ARG K 614 Details of bonding type rmsd hydrogen bonds : bond 0.04683 ( 951) hydrogen bonds : angle 3.10498 ( 2449) covalent geometry : bond 0.00385 (17735) covalent geometry : angle 0.59262 (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: 20 poor density : 151 time to evaluate : 1.441 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8486 (pm20) cc_final: 0.8154 (pm20) REVERT: A 79 LYS cc_start: 0.8567 (tttt) cc_final: 0.8201 (mtpt) REVERT: A 94 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8317 (mm-30) REVERT: C 15 LYS cc_start: 0.8260 (ttpm) cc_final: 0.7922 (ttpt) REVERT: C 92 GLU cc_start: 0.8200 (mt-10) cc_final: 0.7647 (mt-10) REVERT: D 39 TYR cc_start: 0.8485 (t80) cc_final: 0.8056 (t80) REVERT: D 102 GLU cc_start: 0.8009 (pm20) cc_final: 0.7752 (pm20) REVERT: E 97 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7986 (mp0) REVERT: F 93 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.7772 (mp10) REVERT: H 39 TYR cc_start: 0.8323 (t80) cc_final: 0.8034 (t80) REVERT: H 56 MET cc_start: 0.9213 (tpp) cc_final: 0.8941 (tpt) REVERT: H 65 ASP cc_start: 0.8914 (t0) cc_final: 0.8650 (t0) REVERT: H 90 GLU cc_start: 0.8910 (mp0) cc_final: 0.8486 (mp0) REVERT: K 510 LEU cc_start: 0.9524 (tm) cc_final: 0.9211 (pp) REVERT: K 735 GLN cc_start: 0.8701 (pt0) cc_final: 0.8225 (pt0) outliers start: 20 outliers final: 11 residues processed: 163 average time/residue: 1.5259 time to fit residues: 273.0789 Evaluate side-chains 155 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 1.391 ------------------------------------------------------------------------------- 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 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 347 ASN Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR Chi-restraints excluded: chain K residue 596 TYR 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: 2.9990 chunk 121 optimal weight: 0.9990 chunk 155 optimal weight: 3.9990 chunk 40 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 93 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 102 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 = 0.3788 r_free = 0.3788 target = 0.094328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.069500 restraints weight = 46530.542| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.20 r_work: 0.3129 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.2476 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= 0.178 Angle : 0.609 12.183 25206 Z= 0.335 Chirality : 0.036 0.195 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.304 176.717 4684 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 1.99 % Allowed : 21.00 % Favored : 77.01 % 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: 2.21 (0.18), residues: 809 sheet: -1.42 (0.67), residues: 78 loop : -1.33 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 267 HIS 0.013 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.012 0.001 TYR K 596 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04774 ( 951) hydrogen bonds : angle 3.13483 ( 2449) covalent geometry : bond 0.00399 (17735) covalent geometry : angle 0.60854 (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 172 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 149 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8510 (pm20) cc_final: 0.8272 (pm20) REVERT: A 94 GLU cc_start: 0.8600 (OUTLIER) cc_final: 0.8336 (mm-30) REVERT: A 120 MET cc_start: 0.8997 (OUTLIER) cc_final: 0.8487 (mtm) REVERT: B 53 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7384 (mm-30) REVERT: B 74 GLU cc_start: 0.8101 (tp30) cc_final: 0.7800 (mm-30) REVERT: C 15 LYS cc_start: 0.8269 (ttpm) cc_final: 0.7938 (ttpt) REVERT: C 92 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7555 (mt-10) REVERT: D 39 TYR cc_start: 0.8476 (t80) cc_final: 0.8029 (t80) REVERT: E 97 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.7969 (mp0) REVERT: F 93 GLN cc_start: 0.8648 (OUTLIER) cc_final: 0.7803 (mp10) REVERT: H 39 TYR cc_start: 0.8328 (t80) cc_final: 0.8035 (t80) REVERT: H 56 MET cc_start: 0.9200 (tpp) cc_final: 0.8933 (tpt) REVERT: H 65 ASP cc_start: 0.8932 (t0) cc_final: 0.8652 (t0) REVERT: H 90 GLU cc_start: 0.8941 (mp0) cc_final: 0.8516 (mp0) REVERT: K 333 GLU cc_start: 0.8292 (mp0) cc_final: 0.7672 (tm-30) REVERT: K 470 MET cc_start: 0.8503 (tpp) cc_final: 0.8242 (tpt) REVERT: K 510 LEU cc_start: 0.9520 (tm) cc_final: 0.9209 (pp) REVERT: K 735 GLN cc_start: 0.8709 (pt0) cc_final: 0.8254 (pt0) outliers start: 23 outliers final: 12 residues processed: 160 average time/residue: 1.4610 time to fit residues: 256.3486 Evaluate side-chains 159 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 142 time to evaluate : 1.319 ------------------------------------------------------------------------------- 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 D residue 87 THR 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: 10.0000 chunk 152 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 157 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 11 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3816 r_free = 0.3816 target = 0.095486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.070916 restraints weight = 46814.983| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.21 r_work: 0.3170 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3170 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8425 moved from start: 0.2637 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 : 0.603 12.486 25206 Z= 0.331 Chirality : 0.035 0.183 2850 Planarity : 0.003 0.030 2187 Dihedral : 28.232 177.031 4684 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.47 % Allowed : 21.78 % Favored : 76.75 % 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: 1.38 (0.24), residues: 1323 helix: 2.25 (0.18), residues: 809 sheet: -1.37 (0.67), residues: 78 loop : -1.29 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.014 0.001 HIS K 211 PHE 0.014 0.001 PHE K 234 TYR 0.012 0.001 TYR K 596 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04418 ( 951) hydrogen bonds : angle 3.04517 ( 2449) covalent geometry : bond 0.00328 (17735) covalent geometry : angle 0.60313 (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 171 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 154 time to evaluate : 1.491 Fit side-chains revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8936 (mt-10) cc_final: 0.8727 (mt-10) REVERT: A 59 GLU cc_start: 0.8448 (pm20) cc_final: 0.8131 (pm20) REVERT: A 90 MET cc_start: 0.9027 (tpp) cc_final: 0.8802 (mmm) REVERT: A 94 GLU cc_start: 0.8534 (OUTLIER) cc_final: 0.8254 (mm-30) REVERT: A 120 MET cc_start: 0.8978 (OUTLIER) cc_final: 0.8472 (mtm) REVERT: B 53 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7228 (mm-30) REVERT: B 74 GLU cc_start: 0.8027 (tp30) cc_final: 0.7782 (mm-30) REVERT: C 15 LYS cc_start: 0.8250 (ttpm) cc_final: 0.7904 (ttpt) REVERT: C 92 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7777 (mt-10) REVERT: D 39 TYR cc_start: 0.8454 (t80) cc_final: 0.8031 (t80) REVERT: E 97 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7964 (mp0) REVERT: F 93 GLN cc_start: 0.8593 (OUTLIER) cc_final: 0.7754 (mp10) REVERT: H 39 TYR cc_start: 0.8308 (t80) cc_final: 0.8049 (t80) REVERT: H 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8695 (t0) REVERT: H 90 GLU cc_start: 0.8862 (mp0) cc_final: 0.8468 (mp0) REVERT: K 333 GLU cc_start: 0.8306 (mp0) cc_final: 0.7635 (tm-30) REVERT: K 470 MET cc_start: 0.8533 (tpp) cc_final: 0.8307 (tpt) REVERT: K 510 LEU cc_start: 0.9508 (tm) cc_final: 0.9206 (pp) REVERT: K 735 GLN cc_start: 0.8711 (pt0) cc_final: 0.8238 (pt0) outliers start: 17 outliers final: 7 residues processed: 162 average time/residue: 1.5549 time to fit residues: 275.3405 Evaluate side-chains 160 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 148 time to evaluate : 1.359 ------------------------------------------------------------------------------- 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 H residue 29 THR Chi-restraints excluded: chain K residue 211 HIS Chi-restraints excluded: chain K residue 376 SER Chi-restraints excluded: chain K residue 390 THR 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: 6.9990 chunk 156 optimal weight: 7.9990 chunk 149 optimal weight: 6.9990 chunk 62 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 94 optimal weight: 4.9990 chunk 40 optimal weight: 0.7980 chunk 113 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.093482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.068461 restraints weight = 47019.052| |-----------------------------------------------------------------------------| r_work (start): 0.3253 rms_B_bonded: 2.23 r_work: 0.3100 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 17735 Z= 0.228 Angle : 0.647 12.809 25206 Z= 0.353 Chirality : 0.037 0.213 2850 Planarity : 0.004 0.030 2187 Dihedral : 28.418 176.120 4684 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.82 % Allowed : 22.21 % Favored : 75.97 % 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: 1.22 (0.24), residues: 1323 helix: 2.10 (0.18), residues: 809 sheet: -1.51 (0.66), residues: 78 loop : -1.28 (0.29), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 267 HIS 0.022 0.002 HIS K 211 PHE 0.018 0.002 PHE K 234 TYR 0.016 0.001 TYR K 596 ARG 0.008 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.05388 ( 951) hydrogen bonds : angle 3.20253 ( 2449) covalent geometry : bond 0.00517 (17735) covalent geometry : angle 0.64702 (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 169 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.398 Fit side-chains revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8338 (mm-30) REVERT: A 120 MET cc_start: 0.9029 (OUTLIER) cc_final: 0.8532 (mtm) REVERT: B 74 GLU cc_start: 0.8184 (tp30) cc_final: 0.7915 (mm-30) REVERT: C 15 LYS cc_start: 0.8342 (ttpm) cc_final: 0.8032 (ttpt) REVERT: C 92 GLU cc_start: 0.8246 (mt-10) cc_final: 0.8029 (mt-10) REVERT: D 39 TYR cc_start: 0.8536 (t80) cc_final: 0.8005 (t80) REVERT: E 97 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8008 (mp0) REVERT: F 93 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: H 39 TYR cc_start: 0.8316 (t80) cc_final: 0.8055 (t80) REVERT: H 65 ASP cc_start: 0.8928 (t0) cc_final: 0.8646 (t0) REVERT: H 90 GLU cc_start: 0.8967 (mp0) cc_final: 0.8503 (mp0) REVERT: K 470 MET cc_start: 0.8650 (tpp) cc_final: 0.8449 (tpt) REVERT: K 510 LEU cc_start: 0.9502 (tm) cc_final: 0.9208 (pp) outliers start: 21 outliers final: 11 residues processed: 157 average time/residue: 1.5386 time to fit residues: 264.4083 Evaluate side-chains 158 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 143 time to evaluate : 1.458 ------------------------------------------------------------------------------- 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 D residue 87 THR 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 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 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: 0.7980 chunk 39 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 90 optimal weight: 3.9990 chunk 75 optimal weight: 5.9990 chunk 151 optimal weight: 1.9990 chunk 155 optimal weight: 7.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.3807 r_free = 0.3807 target = 0.094996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.070393 restraints weight = 47142.561| |-----------------------------------------------------------------------------| r_work (start): 0.3307 rms_B_bonded: 2.21 r_work: 0.3156 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3156 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8438 moved from start: 0.2584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17735 Z= 0.156 Angle : 0.626 12.770 25206 Z= 0.341 Chirality : 0.036 0.332 2850 Planarity : 0.004 0.029 2187 Dihedral : 28.323 176.732 4684 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 1.30 % Allowed : 22.82 % Favored : 75.89 % 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: 2.17 (0.18), residues: 810 sheet: -1.44 (0.66), residues: 78 loop : -1.24 (0.29), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.012 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.012 0.001 TYR K 596 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04579 ( 951) hydrogen bonds : angle 3.07644 ( 2449) covalent geometry : bond 0.00345 (17735) covalent geometry : angle 0.62577 (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 169 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 1.450 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8480 (pm20) cc_final: 0.8153 (pm20) REVERT: A 79 LYS cc_start: 0.8428 (tttt) cc_final: 0.8179 (mtpt) REVERT: A 90 MET cc_start: 0.9033 (tpp) cc_final: 0.8807 (mmm) REVERT: A 94 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.8295 (mm-30) REVERT: A 120 MET cc_start: 0.8995 (OUTLIER) cc_final: 0.8496 (mtm) REVERT: C 15 LYS cc_start: 0.8291 (ttpm) cc_final: 0.7984 (ttpt) REVERT: C 92 GLU cc_start: 0.8184 (mt-10) cc_final: 0.7893 (mt-10) REVERT: D 39 TYR cc_start: 0.8540 (t80) cc_final: 0.8057 (t80) REVERT: E 97 GLU cc_start: 0.8428 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: F 93 GLN cc_start: 0.8624 (OUTLIER) cc_final: 0.7791 (mp10) REVERT: G 13 LYS cc_start: 0.9075 (tptt) cc_final: 0.8688 (mmmm) REVERT: H 39 TYR cc_start: 0.8324 (t80) cc_final: 0.8053 (t80) REVERT: H 65 ASP cc_start: 0.8950 (t0) cc_final: 0.8676 (t0) REVERT: H 90 GLU cc_start: 0.8891 (mp0) cc_final: 0.8494 (mp0) REVERT: K 93 LYS cc_start: 0.8406 (mptt) cc_final: 0.8096 (mmtt) REVERT: K 333 GLU cc_start: 0.8276 (mp0) cc_final: 0.7887 (tm-30) REVERT: K 510 LEU cc_start: 0.9483 (tm) cc_final: 0.9194 (pp) outliers start: 15 outliers final: 10 residues processed: 159 average time/residue: 1.6165 time to fit residues: 281.7200 Evaluate side-chains 163 residues out of total 1168 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 1.446 ------------------------------------------------------------------------------- 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 D residue 87 THR 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 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 594 VAL Chi-restraints excluded: chain K residue 647 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 158 random chunks: chunk 118 optimal weight: 7.9990 chunk 119 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 94 optimal weight: 4.9990 chunk 147 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 135 GLN 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 = 0.3813 r_free = 0.3813 target = 0.095321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.070865 restraints weight = 46938.018| |-----------------------------------------------------------------------------| r_work (start): 0.3319 rms_B_bonded: 2.21 r_work: 0.3168 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.2728 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= 0.154 Angle : 0.615 12.650 25206 Z= 0.338 Chirality : 0.035 0.300 2850 Planarity : 0.004 0.030 2187 Dihedral : 28.208 177.596 4684 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 1.73 % Allowed : 22.47 % Favored : 75.80 % 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: 1.36 (0.24), residues: 1323 helix: 2.21 (0.18), residues: 808 sheet: -1.43 (0.66), residues: 78 loop : -1.21 (0.29), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.019 0.001 HIS K 211 PHE 0.015 0.001 PHE K 234 TYR 0.014 0.001 TYR K 596 ARG 0.008 0.000 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04467 ( 951) hydrogen bonds : angle 3.04091 ( 2449) covalent geometry : bond 0.00342 (17735) covalent geometry : angle 0.61507 (25206) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9657.47 seconds wall clock time: 167 minutes 2.10 seconds (10022.10 seconds total)