Starting phenix.real_space_refine on Sat Jun 14 09:42:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnt_61626/06_2025/9jnt_61626.cif" } resolution = 2.7 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= 0.011 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 9366 2.51 5 N 2985 2.21 5 O 3612 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 27 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16283 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 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: 4240 Number of conformers: 1 Conformer: "" Number of residues, atoms: 516, 4240 Classifications: {'peptide': 516} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 496} Chain breaks: 3 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: 10.24, per 1000 atoms: 0.63 Number of scatterers: 16283 At special positions: 0 Unit cell: (93.095, 116.91, 158.045, 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 3612 8.00 N 2985 7.00 C 9366 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: 4.31 Conformation dependent library (CDL) restraints added in 1.3 seconds 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2428 Finding SS restraints... Secondary structure from input PDB file: 61 helices and 12 sheets defined 63.5% alpha, 3.6% beta 144 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 6.83 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 removed outlier: 3.643A pdb=" N ARG A 49 " --> pdb=" O THR A 45 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.618A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.605A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.843A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.599A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.465A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.504A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 75 removed outlier: 3.539A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 78 No H-bonds generated for 'chain 'E' and resid 76 through 78' Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.606A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.032A 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 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 88 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.557A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.512A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 4.133A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N HIS H 106 " --> pdb=" O GLU H 102 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA H 107 " --> pdb=" O LEU H 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.857A pdb=" N LYS K 88 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 113 removed outlier: 3.519A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N LYS K 107 " --> pdb=" O GLU K 103 " (cutoff:3.500A) Processing helix chain 'K' and resid 114 through 115 No H-bonds generated for 'chain 'K' and resid 114 through 115' Processing helix chain 'K' and resid 116 through 119 removed outlier: 3.560A pdb=" N PHE K 119 " --> pdb=" O SER K 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 116 through 119' Processing helix chain 'K' and resid 120 through 129 removed outlier: 4.279A pdb=" N ALA K 128 " --> pdb=" O GLU K 124 " (cutoff:3.500A) Processing helix chain 'K' and resid 130 through 136 removed outlier: 4.089A pdb=" N GLN K 135 " --> pdb=" O LYS K 132 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N VAL K 136 " --> pdb=" O PHE K 133 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 212 Processing helix chain 'K' and resid 227 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 268 removed outlier: 4.228A pdb=" N GLU K 263 " --> pdb=" O ASN K 259 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR K 268 " --> pdb=" O ILE K 264 " (cutoff:3.500A) Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 removed outlier: 3.684A pdb=" N ILE K 307 " --> pdb=" O TYR K 303 " (cutoff:3.500A) Processing helix chain 'K' and resid 334 through 343 removed outlier: 3.583A pdb=" N PHE K 343 " --> pdb=" O VAL K 339 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 371 Processing helix chain 'K' and resid 377 through 385 Processing helix chain 'K' and resid 395 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 476 removed outlier: 3.764A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 478 through 482 Processing helix chain 'K' and resid 494 through 498 removed outlier: 3.583A pdb=" N LEU K 497 " --> pdb=" O ASP K 494 " (cutoff:3.500A) Processing helix chain 'K' and resid 501 through 516 removed outlier: 3.550A pdb=" N GLN K 505 " --> pdb=" O ALA K 501 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 542 removed outlier: 3.840A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 566 Processing helix chain 'K' and resid 601 through 614 removed outlier: 4.065A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG K 611 " --> pdb=" O GLN K 607 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 3.770A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 653 through 658 removed outlier: 3.803A pdb=" N SER K 657 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.917A 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: 7.001A 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 101 through 102 removed outlier: 6.958A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.814A 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: 6.976A 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 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 301 through 302 removed outlier: 7.579A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.971A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.009A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 6.288A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 427 through 431 556 hydrogen bonds defined for protein. 1638 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 8.61 Time building geometry restraints manager: 4.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2188 1.32 - 1.44: 5908 1.44 - 1.57: 8450 1.57 - 1.69: 586 1.69 - 1.81: 43 Bond restraints: 17175 Sorted by residual: bond pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.34e-02 5.57e+03 2.57e+01 bond pdb=" CA LEU K 422 " pdb=" C LEU K 422 " ideal model delta sigma weight residual 1.522 1.482 0.040 1.29e-02 6.01e+03 9.38e+00 bond pdb=" C PRO K 423 " pdb=" O PRO K 423 " ideal model delta sigma weight residual 1.232 1.200 0.033 1.20e-02 6.94e+03 7.44e+00 bond pdb=" CA PRO K 423 " pdb=" CB PRO K 423 " ideal model delta sigma weight residual 1.533 1.496 0.036 1.35e-02 5.49e+03 7.26e+00 bond pdb=" N THR K 419 " pdb=" CA THR K 419 " ideal model delta sigma weight residual 1.457 1.425 0.032 1.29e-02 6.01e+03 6.28e+00 ... (remaining 17170 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 23494 1.54 - 3.07: 827 3.07 - 4.61: 108 4.61 - 6.14: 26 6.14 - 7.68: 7 Bond angle restraints: 24462 Sorted by residual: angle pdb=" C LEU K 422 " pdb=" N PRO K 423 " pdb=" CA PRO K 423 " ideal model delta sigma weight residual 120.31 116.64 3.67 9.80e-01 1.04e+00 1.40e+01 angle pdb=" CA PRO K 423 " pdb=" C PRO K 423 " pdb=" N LYS K 424 " ideal model delta sigma weight residual 114.65 119.27 -4.62 1.27e+00 6.20e-01 1.32e+01 angle pdb=" CA PRO K 189 " pdb=" N PRO K 189 " pdb=" CD PRO K 189 " ideal model delta sigma weight residual 112.00 106.92 5.08 1.40e+00 5.10e-01 1.32e+01 angle pdb=" O VAL K 417 " pdb=" C VAL K 417 " pdb=" N GLU K 418 " ideal model delta sigma weight residual 122.71 119.44 3.27 9.70e-01 1.06e+00 1.14e+01 angle pdb=" N VAL B 21 " pdb=" CA VAL B 21 " pdb=" C VAL B 21 " ideal model delta sigma weight residual 112.96 109.73 3.23 1.00e+00 1.00e+00 1.04e+01 ... (remaining 24457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.90: 8160 35.90 - 71.81: 1409 71.81 - 107.71: 19 107.71 - 143.61: 3 143.61 - 179.52: 11 Dihedral angle restraints: 9602 sinusoidal: 5855 harmonic: 3747 Sorted by residual: dihedral pdb=" CA TYR K 545 " pdb=" C TYR K 545 " pdb=" N CYS K 546 " pdb=" CA CYS K 546 " ideal model delta harmonic sigma weight residual 180.00 149.22 30.78 0 5.00e+00 4.00e-02 3.79e+01 dihedral pdb=" CA LEU B 22 " pdb=" C LEU B 22 " pdb=" N ARG B 23 " pdb=" CA ARG B 23 " ideal model delta harmonic sigma weight residual -180.00 -149.85 -30.15 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA HIS B 18 " pdb=" C HIS B 18 " pdb=" N ARG B 19 " pdb=" CA ARG B 19 " ideal model delta harmonic sigma weight residual 180.00 -150.71 -29.29 0 5.00e+00 4.00e-02 3.43e+01 ... (remaining 9599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 2279 0.050 - 0.100: 422 0.100 - 0.150: 71 0.150 - 0.200: 5 0.200 - 0.251: 1 Chirality restraints: 2778 Sorted by residual: chirality pdb=" CA LEU K 421 " pdb=" N LEU K 421 " pdb=" C LEU K 421 " pdb=" CB LEU K 421 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" P DG I 99 " pdb=" OP1 DG I 99 " pdb=" OP2 DG I 99 " pdb=" O5' DG I 99 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.17 2.00e-01 2.50e+01 7.42e-01 chirality pdb=" CG LEU C 63 " pdb=" CB LEU C 63 " pdb=" CD1 LEU C 63 " pdb=" CD2 LEU C 63 " both_signs ideal model delta sigma weight residual False -2.59 -2.76 0.17 2.00e-01 2.50e+01 6.85e-01 ... (remaining 2775 not shown) Planarity restraints: 2087 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER K 188 " -0.075 5.00e-02 4.00e+02 1.11e-01 1.98e+01 pdb=" N PRO K 189 " 0.192 5.00e-02 4.00e+02 pdb=" CA PRO K 189 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO K 189 " -0.059 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 417 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C VAL K 417 " -0.044 2.00e-02 2.50e+03 pdb=" O VAL K 417 " 0.016 2.00e-02 2.50e+03 pdb=" N GLU K 418 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO K 489 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.029 5.00e-02 4.00e+02 ... (remaining 2084 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 118 2.57 - 3.15: 12519 3.15 - 3.73: 28110 3.73 - 4.32: 39262 4.32 - 4.90: 58382 Nonbonded interactions: 138391 Sorted by model distance: nonbonded pdb="MG MG K1201 " pdb=" O2B ADP K1202 " model vdw 1.985 2.170 nonbonded pdb=" O PRO K 372 " pdb=" OG SER K 376 " model vdw 2.123 3.040 nonbonded pdb=" OH TYR K 199 " pdb=" O LEU K 225 " model vdw 2.165 3.040 nonbonded pdb=" O ILE E 119 " pdb=" OG SER F 47 " model vdw 2.190 3.040 nonbonded pdb=" O VAL K 398 " pdb=" ND1 HIS K 402 " model vdw 2.200 3.120 ... (remaining 138386 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 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 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: 1.410 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: 0.600 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 45.360 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:20.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 17175 Z= 0.230 Angle : 0.667 7.680 24462 Z= 0.389 Chirality : 0.040 0.251 2778 Planarity : 0.005 0.111 2087 Dihedral : 26.481 179.516 7174 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.59 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % 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: 0.16 (0.25), residues: 1259 helix: 1.27 (0.19), residues: 768 sheet: -2.43 (0.66), residues: 62 loop : -1.63 (0.30), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 364 HIS 0.006 0.001 HIS D 46 PHE 0.033 0.002 PHE K 381 TYR 0.016 0.001 TYR K 320 ARG 0.004 0.000 ARG A 52 Details of bonding type rmsd hydrogen bonds : bond 0.08890 ( 926) hydrogen bonds : angle 4.10263 ( 2378) covalent geometry : bond 0.00502 (17175) covalent geometry : angle 0.66653 (24462) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 208 time to evaluate : 1.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8898 (pm20) cc_final: 0.8625 (pm20) REVERT: C 104 GLN cc_start: 0.8354 (mm110) cc_final: 0.7799 (mm110) REVERT: D 43 LYS cc_start: 0.9131 (mmtt) cc_final: 0.8911 (mmtt) REVERT: D 90 GLU cc_start: 0.8759 (mp0) cc_final: 0.8406 (mp0) REVERT: E 59 GLU cc_start: 0.8313 (pm20) cc_final: 0.8103 (pm20) REVERT: E 77 ASP cc_start: 0.8668 (m-30) cc_final: 0.8397 (m-30) REVERT: E 106 ASP cc_start: 0.8221 (m-30) cc_final: 0.7948 (m-30) REVERT: G 75 LYS cc_start: 0.8801 (mttm) cc_final: 0.8487 (mmmt) REVERT: H 65 ASP cc_start: 0.8628 (t70) cc_final: 0.8052 (t0) REVERT: K 184 GLN cc_start: 0.8499 (pm20) cc_final: 0.8281 (mp10) REVERT: K 294 CYS cc_start: 0.8331 (m) cc_final: 0.7606 (t) outliers start: 0 outliers final: 0 residues processed: 208 average time/residue: 2.0676 time to fit residues: 463.1740 Evaluate side-chains 155 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 127 optimal weight: 6.9990 chunk 114 optimal weight: 9.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 118 optimal weight: 0.7980 chunk 45 optimal weight: 9.9990 chunk 71 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 137 optimal weight: 5.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN C 104 GLN E 68 GLN F 93 GLN G 73 ASN G 104 GLN K 86 ASN K 111 HIS K 317 ASN K 361 HIS K 617 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.088034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.058005 restraints weight = 37503.193| |-----------------------------------------------------------------------------| r_work (start): 0.2958 rms_B_bonded: 2.34 r_work: 0.2769 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.045 17175 Z= 0.281 Angle : 0.676 8.340 24462 Z= 0.373 Chirality : 0.041 0.164 2778 Planarity : 0.005 0.062 2087 Dihedral : 30.435 177.428 4613 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.37 % Allowed : 11.14 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.31 (0.25), residues: 1259 helix: 1.41 (0.19), residues: 775 sheet: -2.21 (0.65), residues: 69 loop : -1.70 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.014 0.001 PHE K 381 TYR 0.013 0.002 TYR H 34 ARG 0.009 0.001 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.04753 ( 926) hydrogen bonds : angle 3.52900 ( 2378) covalent geometry : bond 0.00652 (17175) covalent geometry : angle 0.67588 (24462) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 1.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.8134 (OUTLIER) cc_final: 0.7581 (p-80) REVERT: A 59 GLU cc_start: 0.8870 (pm20) cc_final: 0.8434 (pm20) REVERT: B 24 ASP cc_start: 0.8367 (t0) cc_final: 0.8160 (t0) REVERT: C 90 ASP cc_start: 0.8399 (t0) cc_final: 0.8130 (t0) REVERT: D 90 GLU cc_start: 0.8861 (mp0) cc_final: 0.8603 (mp0) REVERT: E 59 GLU cc_start: 0.8405 (pm20) cc_final: 0.7885 (pm20) REVERT: E 77 ASP cc_start: 0.9023 (m-30) cc_final: 0.8747 (m-30) REVERT: E 106 ASP cc_start: 0.8460 (m-30) cc_final: 0.8210 (m-30) REVERT: E 123 ASP cc_start: 0.9120 (m-30) cc_final: 0.8889 (m-30) REVERT: G 64 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.7963 (tt0) REVERT: H 65 ASP cc_start: 0.8753 (t70) cc_final: 0.8215 (t0) REVERT: K 294 CYS cc_start: 0.8127 (m) cc_final: 0.7313 (t) REVERT: K 568 ASP cc_start: 0.8432 (p0) cc_final: 0.8216 (p0) REVERT: K 655 ARG cc_start: 0.8324 (pmt-80) cc_final: 0.8086 (pmt-80) outliers start: 26 outliers final: 14 residues processed: 181 average time/residue: 1.8309 time to fit residues: 357.1484 Evaluate side-chains 173 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 157 time to evaluate : 1.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 138 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 126 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 84 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.090169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060480 restraints weight = 37069.298| |-----------------------------------------------------------------------------| r_work (start): 0.3003 rms_B_bonded: 2.28 r_work: 0.2816 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 17175 Z= 0.150 Angle : 0.629 9.165 24462 Z= 0.349 Chirality : 0.038 0.167 2778 Planarity : 0.004 0.052 2087 Dihedral : 30.342 176.723 4613 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.10 % Allowed : 14.52 % Favored : 83.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.51 (0.25), residues: 1259 helix: 1.59 (0.19), residues: 777 sheet: -2.11 (0.67), residues: 69 loop : -1.69 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.011 0.001 PHE K 574 TYR 0.011 0.001 TYR F 51 ARG 0.006 0.000 ARG D 96 Details of bonding type rmsd hydrogen bonds : bond 0.03976 ( 926) hydrogen bonds : angle 3.30468 ( 2378) covalent geometry : bond 0.00331 (17175) covalent geometry : angle 0.62929 (24462) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 173 time to evaluate : 1.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8844 (pm20) cc_final: 0.8384 (pm20) REVERT: A 81 ASP cc_start: 0.8707 (t0) cc_final: 0.8496 (t0) REVERT: B 24 ASP cc_start: 0.8372 (t0) cc_final: 0.8163 (t0) REVERT: E 59 GLU cc_start: 0.8453 (pm20) cc_final: 0.7953 (pm20) REVERT: E 77 ASP cc_start: 0.9019 (m-30) cc_final: 0.8741 (m-30) REVERT: E 105 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7760 (mt-10) REVERT: E 123 ASP cc_start: 0.9112 (m-30) cc_final: 0.8885 (m-30) REVERT: F 85 ASP cc_start: 0.8844 (m-30) cc_final: 0.8596 (m-30) REVERT: G 64 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.7927 (tt0) REVERT: G 73 ASN cc_start: 0.8378 (m-40) cc_final: 0.7748 (t0) REVERT: H 65 ASP cc_start: 0.8731 (t70) cc_final: 0.8114 (t0) REVERT: K 294 CYS cc_start: 0.8041 (m) cc_final: 0.7211 (t) REVERT: K 568 ASP cc_start: 0.8347 (p0) cc_final: 0.8083 (p0) REVERT: K 655 ARG cc_start: 0.8394 (pmt-80) cc_final: 0.8157 (pmt-80) outliers start: 23 outliers final: 12 residues processed: 182 average time/residue: 1.7557 time to fit residues: 345.8329 Evaluate side-chains 174 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 335 MET Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 119 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 48 optimal weight: 2.9990 chunk 148 optimal weight: 6.9990 chunk 37 optimal weight: 0.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 15 optimal weight: 5.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN K 505 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.060105 restraints weight = 37472.873| |-----------------------------------------------------------------------------| r_work (start): 0.2983 rms_B_bonded: 2.26 r_work: 0.2796 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.1217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17175 Z= 0.210 Angle : 0.625 8.624 24462 Z= 0.348 Chirality : 0.038 0.161 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.155 176.492 4613 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 2.83 % Allowed : 14.25 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.58 (0.25), residues: 1259 helix: 1.63 (0.19), residues: 776 sheet: -2.22 (0.65), residues: 69 loop : -1.57 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.006 0.001 HIS K 613 PHE 0.009 0.001 PHE K 381 TYR 0.010 0.001 TYR H 34 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04213 ( 926) hydrogen bonds : angle 3.23855 ( 2378) covalent geometry : bond 0.00481 (17175) covalent geometry : angle 0.62474 (24462) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 168 time to evaluate : 1.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8856 (pm20) cc_final: 0.8367 (pm20) REVERT: A 81 ASP cc_start: 0.8834 (t0) cc_final: 0.8546 (t0) REVERT: B 24 ASP cc_start: 0.8412 (t0) cc_final: 0.8173 (t0) REVERT: D 68 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8102 (tp30) REVERT: D 90 GLU cc_start: 0.8843 (mp0) cc_final: 0.8563 (mp0) REVERT: E 59 GLU cc_start: 0.8482 (pm20) cc_final: 0.7918 (pm20) REVERT: E 77 ASP cc_start: 0.9012 (m-30) cc_final: 0.8736 (m-30) REVERT: E 123 ASP cc_start: 0.9089 (m-30) cc_final: 0.8854 (m-30) REVERT: F 85 ASP cc_start: 0.8830 (m-30) cc_final: 0.8522 (m-30) REVERT: G 64 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.7942 (tt0) REVERT: G 73 ASN cc_start: 0.8375 (m-40) cc_final: 0.7811 (t0) REVERT: H 65 ASP cc_start: 0.8731 (t70) cc_final: 0.8220 (t0) REVERT: K 91 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8362 (tp) REVERT: K 196 LEU cc_start: 0.8938 (tt) cc_final: 0.8698 (tt) REVERT: K 263 GLU cc_start: 0.9191 (OUTLIER) cc_final: 0.8889 (mp0) REVERT: K 294 CYS cc_start: 0.8173 (m) cc_final: 0.7302 (t) REVERT: K 385 PHE cc_start: 0.6551 (t80) cc_final: 0.6001 (t80) REVERT: K 568 ASP cc_start: 0.8278 (p0) cc_final: 0.7987 (p0) outliers start: 31 outliers final: 19 residues processed: 186 average time/residue: 1.6616 time to fit residues: 334.3866 Evaluate side-chains 184 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 161 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 91 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 92 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 40 optimal weight: 0.5980 chunk 89 optimal weight: 5.9990 chunk 140 optimal weight: 5.9990 chunk 94 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 114 optimal weight: 3.9990 chunk 128 optimal weight: 10.0000 chunk 37 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 overall best weight: 2.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.089878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3008 r_free = 0.3008 target = 0.059989 restraints weight = 37720.283| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.29 r_work: 0.2793 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 17175 Z= 0.215 Angle : 0.623 7.961 24462 Z= 0.347 Chirality : 0.038 0.158 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.083 177.083 4613 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.29 % Allowed : 15.43 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.58 (0.25), residues: 1259 helix: 1.65 (0.19), residues: 778 sheet: -2.27 (0.64), residues: 69 loop : -1.63 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 PHE 0.008 0.001 PHE B 61 TYR 0.011 0.001 TYR H 34 ARG 0.005 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04178 ( 926) hydrogen bonds : angle 3.17821 ( 2378) covalent geometry : bond 0.00494 (17175) covalent geometry : angle 0.62330 (24462) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 170 time to evaluate : 2.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8810 (pm20) cc_final: 0.8384 (pm20) REVERT: A 79 LYS cc_start: 0.8889 (tttm) cc_final: 0.8593 (tttp) REVERT: B 24 ASP cc_start: 0.8434 (t0) cc_final: 0.8190 (t0) REVERT: D 68 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8084 (tp30) REVERT: D 90 GLU cc_start: 0.8851 (mp0) cc_final: 0.8629 (mp0) REVERT: E 59 GLU cc_start: 0.8413 (pm20) cc_final: 0.7795 (pm20) REVERT: E 77 ASP cc_start: 0.9014 (m-30) cc_final: 0.8738 (m-30) REVERT: E 123 ASP cc_start: 0.9106 (m-30) cc_final: 0.8885 (m-30) REVERT: F 85 ASP cc_start: 0.8847 (m-30) cc_final: 0.8521 (m-30) REVERT: G 64 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.7945 (tt0) REVERT: G 73 ASN cc_start: 0.8375 (m-40) cc_final: 0.7718 (t0) REVERT: H 65 ASP cc_start: 0.8739 (t70) cc_final: 0.8235 (t0) REVERT: K 196 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8665 (tt) REVERT: K 263 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.8984 (mp0) REVERT: K 385 PHE cc_start: 0.6443 (t80) cc_final: 0.5936 (t80) REVERT: K 568 ASP cc_start: 0.8292 (p0) cc_final: 0.8020 (p0) outliers start: 36 outliers final: 23 residues processed: 189 average time/residue: 1.7368 time to fit residues: 356.4870 Evaluate side-chains 189 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 162 time to evaluate : 1.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 91 optimal weight: 4.9990 chunk 138 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 110 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 54 optimal weight: 0.0470 chunk 66 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN G 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.090907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.061143 restraints weight = 37296.785| |-----------------------------------------------------------------------------| r_work (start): 0.2991 rms_B_bonded: 2.29 r_work: 0.2805 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17175 Z= 0.150 Angle : 0.620 9.280 24462 Z= 0.345 Chirality : 0.037 0.186 2778 Planarity : 0.004 0.056 2087 Dihedral : 30.064 176.708 4613 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.74 % Allowed : 17.44 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.71 (0.25), residues: 1259 helix: 1.76 (0.19), residues: 774 sheet: -2.21 (0.64), residues: 69 loop : -1.59 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.005 0.001 HIS K 613 PHE 0.008 0.001 PHE A 78 TYR 0.010 0.001 TYR C 57 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03866 ( 926) hydrogen bonds : angle 3.11999 ( 2378) covalent geometry : bond 0.00335 (17175) covalent geometry : angle 0.62046 (24462) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 173 time to evaluate : 1.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8797 (pm20) cc_final: 0.8365 (pm20) REVERT: B 24 ASP cc_start: 0.8402 (t0) cc_final: 0.8172 (t0) REVERT: D 68 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8081 (tp30) REVERT: D 90 GLU cc_start: 0.8836 (mp0) cc_final: 0.8589 (mp0) REVERT: E 59 GLU cc_start: 0.8444 (pm20) cc_final: 0.7860 (pm20) REVERT: E 77 ASP cc_start: 0.9010 (m-30) cc_final: 0.8728 (m-30) REVERT: G 64 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7909 (tt0) REVERT: G 73 ASN cc_start: 0.8347 (m-40) cc_final: 0.7737 (t0) REVERT: H 65 ASP cc_start: 0.8683 (t70) cc_final: 0.8124 (t0) REVERT: K 196 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8662 (tt) REVERT: K 263 GLU cc_start: 0.9220 (OUTLIER) cc_final: 0.8897 (mp0) REVERT: K 320 TYR cc_start: 0.8133 (OUTLIER) cc_final: 0.7928 (m-80) REVERT: K 385 PHE cc_start: 0.6418 (t80) cc_final: 0.5930 (t80) REVERT: K 568 ASP cc_start: 0.8292 (p0) cc_final: 0.8036 (p0) outliers start: 30 outliers final: 20 residues processed: 187 average time/residue: 1.9531 time to fit residues: 397.1593 Evaluate side-chains 189 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 164 time to evaluate : 1.555 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 51 LEU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 55 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 16 optimal weight: 3.9990 chunk 59 optimal weight: 0.0370 chunk 52 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 136 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 117 optimal weight: 0.9990 chunk 78 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 overall best weight: 1.3264 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.061164 restraints weight = 37146.823| |-----------------------------------------------------------------------------| r_work (start): 0.2992 rms_B_bonded: 2.29 r_work: 0.2807 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8286 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 17175 Z= 0.173 Angle : 0.616 8.651 24462 Z= 0.342 Chirality : 0.037 0.159 2778 Planarity : 0.004 0.055 2087 Dihedral : 29.914 176.565 4613 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 3.47 % Allowed : 17.90 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.78 (0.25), residues: 1259 helix: 1.82 (0.19), residues: 773 sheet: -2.18 (0.65), residues: 69 loop : -1.55 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.004 0.001 HIS K 613 PHE 0.007 0.001 PHE B 61 TYR 0.009 0.001 TYR C 57 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03791 ( 926) hydrogen bonds : angle 3.06410 ( 2378) covalent geometry : bond 0.00392 (17175) covalent geometry : angle 0.61618 (24462) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 166 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8796 (pm20) cc_final: 0.8361 (pm20) REVERT: B 24 ASP cc_start: 0.8400 (t0) cc_final: 0.8197 (t0) REVERT: D 68 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.8071 (tp30) REVERT: D 90 GLU cc_start: 0.8836 (mp0) cc_final: 0.8573 (mp0) REVERT: E 59 GLU cc_start: 0.8508 (pm20) cc_final: 0.7935 (pm20) REVERT: E 77 ASP cc_start: 0.9004 (m-30) cc_final: 0.8732 (m-30) REVERT: F 85 ASP cc_start: 0.8848 (m-30) cc_final: 0.8627 (m-30) REVERT: G 64 GLU cc_start: 0.8322 (OUTLIER) cc_final: 0.7924 (tt0) REVERT: G 73 ASN cc_start: 0.8265 (m-40) cc_final: 0.7617 (t0) REVERT: G 75 LYS cc_start: 0.8570 (mttm) cc_final: 0.8312 (mmmt) REVERT: H 65 ASP cc_start: 0.8674 (t70) cc_final: 0.8174 (t0) REVERT: K 196 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8660 (tt) REVERT: K 263 GLU cc_start: 0.9241 (OUTLIER) cc_final: 0.9009 (mp0) REVERT: K 299 VAL cc_start: 0.8796 (OUTLIER) cc_final: 0.8544 (p) REVERT: K 385 PHE cc_start: 0.6388 (t80) cc_final: 0.5944 (t80) REVERT: K 568 ASP cc_start: 0.8251 (p0) cc_final: 0.7979 (p0) outliers start: 38 outliers final: 23 residues processed: 185 average time/residue: 2.0739 time to fit residues: 416.7771 Evaluate side-chains 187 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 159 time to evaluate : 1.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 263 GLU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 63 optimal weight: 4.9990 chunk 42 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 94 optimal weight: 4.9990 chunk 117 optimal weight: 5.9990 chunk 45 optimal weight: 10.0000 chunk 110 optimal weight: 8.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.089745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.059835 restraints weight = 37262.763| |-----------------------------------------------------------------------------| r_work (start): 0.2968 rms_B_bonded: 2.29 r_work: 0.2779 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 17175 Z= 0.235 Angle : 0.645 8.266 24462 Z= 0.356 Chirality : 0.039 0.154 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.050 177.296 4613 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 3.20 % Allowed : 18.45 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.70 (0.25), residues: 1259 helix: 1.78 (0.19), residues: 773 sheet: -2.18 (0.65), residues: 69 loop : -1.63 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.005 0.001 HIS D 46 PHE 0.008 0.001 PHE A 78 TYR 0.014 0.001 TYR K 320 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 926) hydrogen bonds : angle 3.15856 ( 2378) covalent geometry : bond 0.00544 (17175) covalent geometry : angle 0.64545 (24462) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8840 (pm20) cc_final: 0.8332 (pm20) REVERT: B 24 ASP cc_start: 0.8440 (t0) cc_final: 0.8227 (t0) REVERT: C 90 ASP cc_start: 0.8357 (t0) cc_final: 0.7971 (t0) REVERT: D 68 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.8072 (tp30) REVERT: D 90 GLU cc_start: 0.8886 (mp0) cc_final: 0.8578 (mp0) REVERT: E 59 GLU cc_start: 0.8434 (pm20) cc_final: 0.7804 (pm20) REVERT: E 77 ASP cc_start: 0.8990 (m-30) cc_final: 0.8710 (m-30) REVERT: G 64 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.7955 (tt0) REVERT: G 73 ASN cc_start: 0.8389 (m-40) cc_final: 0.7631 (t0) REVERT: G 75 LYS cc_start: 0.8608 (mttm) cc_final: 0.8349 (mmmt) REVERT: H 65 ASP cc_start: 0.8750 (t70) cc_final: 0.8199 (t0) REVERT: K 196 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8649 (tt) REVERT: K 299 VAL cc_start: 0.8766 (OUTLIER) cc_final: 0.8482 (p) REVERT: K 385 PHE cc_start: 0.6459 (t80) cc_final: 0.5940 (t80) REVERT: K 568 ASP cc_start: 0.8284 (p0) cc_final: 0.8046 (p0) outliers start: 35 outliers final: 23 residues processed: 181 average time/residue: 2.0502 time to fit residues: 401.6908 Evaluate side-chains 188 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 161 time to evaluate : 1.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Chi-restraints excluded: chain K residue 593 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 36 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 89 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 123 optimal weight: 4.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 0.4980 chunk 120 optimal weight: 7.9990 chunk 40 optimal weight: 0.5980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3577 r_free = 0.3577 target = 0.090553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.060733 restraints weight = 37089.169| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.29 r_work: 0.2791 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17175 Z= 0.164 Angle : 0.648 10.662 24462 Z= 0.356 Chirality : 0.037 0.244 2778 Planarity : 0.004 0.055 2087 Dihedral : 30.043 177.132 4613 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 2.92 % Allowed : 19.27 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.73 (0.25), residues: 1259 helix: 1.80 (0.19), residues: 773 sheet: -2.12 (0.65), residues: 69 loop : -1.62 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 364 HIS 0.004 0.001 HIS A 39 PHE 0.007 0.001 PHE K 381 TYR 0.015 0.001 TYR K 320 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 926) hydrogen bonds : angle 3.13069 ( 2378) covalent geometry : bond 0.00373 (17175) covalent geometry : angle 0.64838 (24462) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 166 time to evaluate : 1.572 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8843 (pm20) cc_final: 0.8384 (pm20) REVERT: B 24 ASP cc_start: 0.8419 (t0) cc_final: 0.8192 (t0) REVERT: C 90 ASP cc_start: 0.8307 (t0) cc_final: 0.7940 (t0) REVERT: D 90 GLU cc_start: 0.8868 (mp0) cc_final: 0.8565 (mp0) REVERT: E 59 GLU cc_start: 0.8459 (pm20) cc_final: 0.7807 (pm20) REVERT: E 77 ASP cc_start: 0.9015 (m-30) cc_final: 0.8743 (m-30) REVERT: G 64 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: G 73 ASN cc_start: 0.8344 (m-40) cc_final: 0.7616 (t0) REVERT: G 75 LYS cc_start: 0.8587 (mttm) cc_final: 0.8336 (mmmt) REVERT: H 65 ASP cc_start: 0.8738 (t70) cc_final: 0.8236 (t0) REVERT: K 196 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8643 (tt) REVERT: K 299 VAL cc_start: 0.8731 (OUTLIER) cc_final: 0.8462 (p) REVERT: K 385 PHE cc_start: 0.6340 (t80) cc_final: 0.5927 (t80) REVERT: K 568 ASP cc_start: 0.8266 (p0) cc_final: 0.8039 (p0) outliers start: 32 outliers final: 23 residues processed: 177 average time/residue: 2.1109 time to fit residues: 407.7663 Evaluate side-chains 186 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 102 ILE Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 121 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 100 optimal weight: 20.0000 chunk 84 optimal weight: 6.9990 chunk 86 optimal weight: 8.9990 chunk 106 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 59 optimal weight: 0.0980 chunk 117 optimal weight: 0.9980 overall best weight: 0.6302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.090894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.061058 restraints weight = 37302.500| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.30 r_work: 0.2803 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 17175 Z= 0.155 Angle : 0.642 11.808 24462 Z= 0.353 Chirality : 0.037 0.290 2778 Planarity : 0.004 0.056 2087 Dihedral : 29.990 177.094 4613 Min Nonbonded Distance : 1.953 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 2.56 % Allowed : 19.54 % Favored : 77.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.80 (0.25), residues: 1259 helix: 1.83 (0.19), residues: 773 sheet: -1.87 (0.68), residues: 66 loop : -1.60 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 364 HIS 0.004 0.001 HIS K 211 PHE 0.007 0.001 PHE B 61 TYR 0.014 0.001 TYR K 320 ARG 0.007 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.03849 ( 926) hydrogen bonds : angle 3.11339 ( 2378) covalent geometry : bond 0.00349 (17175) covalent geometry : angle 0.64181 (24462) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2518 Ramachandran restraints generated. 1259 Oldfield, 0 Emsley, 1259 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 164 time to evaluate : 1.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8792 (pm20) cc_final: 0.8352 (pm20) REVERT: B 24 ASP cc_start: 0.8411 (t0) cc_final: 0.8182 (t0) REVERT: C 90 ASP cc_start: 0.8321 (t0) cc_final: 0.7985 (t0) REVERT: D 90 GLU cc_start: 0.8840 (mp0) cc_final: 0.8531 (mp0) REVERT: E 59 GLU cc_start: 0.8454 (pm20) cc_final: 0.7843 (pm20) REVERT: E 77 ASP cc_start: 0.9017 (m-30) cc_final: 0.8746 (m-30) REVERT: G 64 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.7913 (tt0) REVERT: G 73 ASN cc_start: 0.8328 (m-40) cc_final: 0.7631 (t0) REVERT: G 75 LYS cc_start: 0.8587 (mttm) cc_final: 0.8323 (mmmt) REVERT: H 65 ASP cc_start: 0.8695 (t70) cc_final: 0.8141 (t0) REVERT: K 196 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8628 (tt) REVERT: K 299 VAL cc_start: 0.8780 (OUTLIER) cc_final: 0.8529 (p) REVERT: K 385 PHE cc_start: 0.6356 (t80) cc_final: 0.5900 (t80) REVERT: K 568 ASP cc_start: 0.8261 (p0) cc_final: 0.8031 (p0) outliers start: 28 outliers final: 22 residues processed: 176 average time/residue: 2.0802 time to fit residues: 396.7100 Evaluate side-chains 187 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 162 time to evaluate : 1.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 105 GLU Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 104 GLN Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain K residue 196 LEU Chi-restraints excluded: chain K residue 299 VAL Chi-restraints excluded: chain K residue 327 HIS Chi-restraints excluded: chain K residue 398 VAL Chi-restraints excluded: chain K residue 409 LEU Chi-restraints excluded: chain K residue 475 CYS Chi-restraints excluded: chain K residue 504 LEU Chi-restraints excluded: chain K residue 516 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 151 random chunks: chunk 134 optimal weight: 5.9990 chunk 75 optimal weight: 5.9990 chunk 76 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 99 optimal weight: 6.9990 chunk 145 optimal weight: 0.9980 chunk 101 optimal weight: 7.9990 chunk 148 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 120 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.089637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.059697 restraints weight = 37441.024| |-----------------------------------------------------------------------------| r_work (start): 0.2915 rms_B_bonded: 2.30 r_work: 0.2715 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 17175 Z= 0.255 Angle : 0.665 10.029 24462 Z= 0.365 Chirality : 0.040 0.244 2778 Planarity : 0.004 0.056 2087 Dihedral : 30.008 177.277 4613 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.92 % Allowed : 19.09 % Favored : 77.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: 0.69 (0.24), residues: 1259 helix: 1.75 (0.19), residues: 773 sheet: -1.93 (0.67), residues: 66 loop : -1.65 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 364 HIS 0.005 0.001 HIS D 46 PHE 0.022 0.001 PHE A 78 TYR 0.014 0.001 TYR A 54 ARG 0.006 0.000 ARG F 95 Details of bonding type rmsd hydrogen bonds : bond 0.04419 ( 926) hydrogen bonds : angle 3.18790 ( 2378) covalent geometry : bond 0.00591 (17175) covalent geometry : angle 0.66462 (24462) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12742.33 seconds wall clock time: 229 minutes 0.94 seconds (13740.94 seconds total)