Starting phenix.real_space_refine on Thu Aug 6 14:52:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.58 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jhg_36265/08_2026/8jhg_36265.cif" } resolution = 3.58 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1777 atoms to isotropic. 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 Zn 1 6.06 5 P 320 5.49 5 S 35 5.16 5 C 8303 2.51 5 N 2767 2.21 5 O 3403 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14829 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2019 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Conformer: "B" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'TRP:plan': 1, 'ARG:plan': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 bond proxies already assigned to first conformer: 2045 Chain: "A" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 826 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 854 Classifications: {'peptide': 110} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 104} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 892 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 5, 'TRANS': 109} Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3253 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3307 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1731 SG CYS K 319 83.419 30.899 85.584 1.00159.41 S ATOM 1746 SG CYS K 321 84.413 34.101 84.485 1.00163.58 S Time building chain proxies: 3.17, per 1000 atoms: 0.21 Number of scatterers: 14829 At special positions: 0 Unit cell: (110.4, 123.28, 141.68, 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) Zn 1 29.99 S 35 16.00 P 320 15.00 O 3403 8.00 N 2767 7.00 C 8303 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: 1.22 Conformation dependent library (CDL) restraints added in 527.5 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1944 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 59.5% alpha, 3.1% beta 130 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 2.00 Creating SS restraints... Processing helix chain 'K' and resid 77 through 89 Processing helix chain 'K' and resid 89 through 94 Processing helix chain 'K' and resid 140 through 147 removed outlier: 3.603A pdb=" N PHE K 144 " --> pdb=" O VAL K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 171 through 188 Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'K' and resid 356 through 361 Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.716A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.877A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.994A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N HIS A 113 " --> pdb=" O LEU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 114 through 116 No H-bonds generated for 'chain 'A' and resid 114 through 116' Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.605A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.538A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.547A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.701A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ALA C 52 " --> pdb=" O PRO C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.511A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.709A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.670A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 removed outlier: 3.596A pdb=" N HIS D 106 " --> pdb=" O GLU D 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 55 removed outlier: 3.529A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.761A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.728A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.519A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.713A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.705A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 removed outlier: 3.725A pdb=" N ALA G 21 " --> pdb=" O ARG G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.579A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.594A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'G' and resid 124 through 128 removed outlier: 3.546A pdb=" N LYS G 127 " --> pdb=" O HIS G 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.691A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.704A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 115 Processing helix chain 'H' and resid 116 through 121 removed outlier: 4.041A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 196 through 199 removed outlier: 3.590A pdb=" N LEU K 198 " --> pdb=" O LYS K 211 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 231 through 233 removed outlier: 3.991A pdb=" N MET F 20 " --> pdb=" O VAL K 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.702A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.555A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.818A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.646A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.390A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 418 hydrogen bonds defined for protein. 1242 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 338 hydrogen bonds 676 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 3.09 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3140 1.33 - 1.45: 4873 1.45 - 1.57: 7043 1.57 - 1.69: 638 1.69 - 1.81: 55 Bond restraints: 15749 Sorted by residual: bond pdb=" C3' DA J 161 " pdb=" C2' DA J 161 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.27e+01 bond pdb=" C3' DT J 138 " pdb=" C2' DT J 138 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.19e+01 bond pdb=" C3' DT J 106 " pdb=" C2' DT J 106 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DG J 105 " pdb=" C2' DG J 105 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DC I 55 " pdb=" C2' DC I 55 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 15744 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 21626 1.83 - 3.66: 943 3.66 - 5.49: 42 5.49 - 7.32: 8 7.32 - 9.15: 4 Bond angle restraints: 22623 Sorted by residual: angle pdb=" CA ARG K 352 " pdb=" C ARG K 352 " pdb=" O ARG K 352 " ideal model delta sigma weight residual 121.58 116.35 5.23 1.16e+00 7.43e-01 2.03e+01 angle pdb=" N3 DT I 98 " pdb=" C4 DT I 98 " pdb=" O4 DT I 98 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.92e+01 angle pdb=" N3 DT I 85 " pdb=" C4 DT I 85 " pdb=" O4 DT I 85 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 angle pdb=" O4' DG J 116 " pdb=" C4' DG J 116 " pdb=" C3' DG J 116 " ideal model delta sigma weight residual 106.00 103.41 2.59 6.00e-01 2.78e+00 1.86e+01 angle pdb=" N3 DT I 127 " pdb=" C4 DT I 127 " pdb=" O4 DT I 127 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.83e+01 ... (remaining 22618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.94: 7124 34.94 - 69.87: 1521 69.87 - 104.81: 19 104.81 - 139.74: 1 139.74 - 174.68: 3 Dihedral angle restraints: 8668 sinusoidal: 5654 harmonic: 3014 Sorted by residual: dihedral pdb=" CA ARG F 19 " pdb=" C ARG F 19 " pdb=" N MET F 20 " pdb=" CA MET F 20 " ideal model delta harmonic sigma weight residual -180.00 -159.64 -20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" C4' DT I 99 " pdb=" C3' DT I 99 " pdb=" O3' DT I 99 " pdb=" P DA I 100 " ideal model delta sinusoidal sigma weight residual -140.00 34.68 -174.68 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 138 " pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " pdb=" P DC J 139 " ideal model delta sinusoidal sigma weight residual 220.00 66.35 153.65 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8665 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1456 0.032 - 0.064: 727 0.064 - 0.096: 259 0.096 - 0.128: 97 0.128 - 0.160: 9 Chirality restraints: 2548 Sorted by residual: chirality pdb=" C2' SAM K 402 " pdb=" C1' SAM K 402 " pdb=" C3' SAM K 402 " pdb=" O2' SAM K 402 " both_signs ideal model delta sigma weight residual False -2.76 -2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" C1' DA J 161 " pdb=" O4' DA J 161 " pdb=" C2' DA J 161 " pdb=" N9 DA J 161 " both_signs ideal model delta sigma weight residual False 2.43 2.27 0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CA LYS B 31 " pdb=" N LYS B 31 " pdb=" C LYS B 31 " pdb=" CB LYS B 31 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.49e-01 ... (remaining 2545 not shown) Planarity restraints: 1763 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG K 352 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ARG K 352 " 0.071 2.00e-02 2.50e+03 pdb=" O ARG K 352 " -0.026 2.00e-02 2.50e+03 pdb=" N GLU K 353 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU K 198 " -0.036 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO K 199 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO K 199 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO K 199 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DA J 161 " 0.021 2.00e-02 2.50e+03 1.33e-02 4.84e+00 pdb=" N9 DA J 161 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA J 161 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA J 161 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DA J 161 " 0.004 2.00e-02 2.50e+03 pdb=" C6 DA J 161 " 0.010 2.00e-02 2.50e+03 pdb=" N6 DA J 161 " 0.004 2.00e-02 2.50e+03 pdb=" N1 DA J 161 " -0.018 2.00e-02 2.50e+03 pdb=" C2 DA J 161 " 0.015 2.00e-02 2.50e+03 pdb=" N3 DA J 161 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA J 161 " -0.004 2.00e-02 2.50e+03 ... (remaining 1760 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 590 2.70 - 3.25: 13135 3.25 - 3.80: 25464 3.80 - 4.35: 31687 4.35 - 4.90: 46568 Nonbonded interactions: 117444 Sorted by model distance: nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.152 3.040 nonbonded pdb=" OG SER K 255 " pdb=" O LYS K 258 " model vdw 2.171 3.040 nonbonded pdb=" O SER K 193 " pdb=" NZ LYS K 216 " model vdw 2.178 3.120 nonbonded pdb=" N2 DG J 159 " pdb=" O6 DG J 160 " model vdw 2.217 3.120 nonbonded pdb=" N3 DT I 7 " pdb=" O2 DT J 162 " model vdw 2.263 3.120 ... (remaining 117439 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 38 through 134) selection = (chain 'E' and ((resid 38 through 39 and (name N or name CA or name C or name O \ or name CB )) or resid 40 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and (resid 15 through 75 or (resid 76 and (name N or name CA or name \ C or name O or name CB )) or resid 77 through 124)) } ncs_group { reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 122)) selection = chain 'H' } 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.520 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 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 0.058 15751 Z= 0.486 Angle : 0.743 9.152 22623 Z= 0.630 Chirality : 0.044 0.160 2548 Planarity : 0.004 0.055 1763 Dihedral : 26.864 174.678 6724 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.40 % Favored : 94.60 % Rotamer: Outliers : 0.92 % Allowed : 0.58 % Favored : 98.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.29 (0.27), residues: 1019 helix: 1.78 (0.22), residues: 578 sheet: -2.95 (0.87), residues: 26 loop : -2.00 (0.27), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 40 TYR 0.028 0.001 TYR F 88 PHE 0.008 0.001 PHE K 281 TRP 0.005 0.001 TRP K 218 HIS 0.006 0.001 HIS K 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.49 (15749) covalent geometry : angle 0.74272 / 0.63 (22623) hydrogen bonds : bond 0.13017 / 8.58 ( 756) hydrogen bonds : angle 4.75736 / 3.37 ( 1918) metal coordination : bond 0.00103 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 163 time to evaluate : 0.423 Fit side-chains REVERT: K 100 MET cc_start: 0.7207 (pmm) cc_final: 0.6841 (pmm) REVERT: K 218 TRP cc_start: 0.5099 (OUTLIER) cc_final: 0.4635 (p90) REVERT: K 253 MET cc_start: 0.8311 (mtp) cc_final: 0.7931 (mmp) REVERT: K 294 LEU cc_start: 0.6562 (tp) cc_final: 0.5562 (tp) REVERT: F 88 TYR cc_start: 0.8973 (m-80) cc_final: 0.8549 (m-80) outliers start: 8 outliers final: 0 residues processed: 167 average time/residue: 0.1388 time to fit residues: 33.5286 Evaluate side-chains 140 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 139 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 218 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 98 optimal weight: 4.9990 chunk 107 optimal weight: 30.0000 chunk 10 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 50.0000 chunk 124 optimal weight: 30.0000 chunk 103 optimal weight: 40.0000 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 18 HIS H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.110428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.073417 restraints weight = 38100.908| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075313 restraints weight = 20263.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076534 restraints weight = 14262.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 55)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077217 restraints weight = 11839.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077544 restraints weight = 10774.744| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3150 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3150 r_free = 0.3150 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3150 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.0878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15751 Z= 0.180 Angle : 0.641 8.675 22623 Z= 0.377 Chirality : 0.044 0.264 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.730 170.533 4680 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.04 % Allowed : 9.47 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.26), residues: 1019 helix: 1.98 (0.22), residues: 589 sheet: -2.61 (0.94), residues: 26 loop : -2.14 (0.27), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 352 TYR 0.031 0.002 TYR F 88 PHE 0.011 0.001 PHE K 311 TRP 0.006 0.001 TRP K 218 HIS 0.006 0.001 HIS K 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (15749) covalent geometry : angle 0.64120 / 0.38 (22623) hydrogen bonds : bond 0.06668 / 4.50 ( 756) hydrogen bonds : angle 3.65482 / 2.59 ( 1918) metal coordination : bond 0.00190 / 0.10 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 139 time to evaluate : 0.397 Fit side-chains REVERT: K 100 MET cc_start: 0.7108 (pmm) cc_final: 0.6660 (pmm) REVERT: K 218 TRP cc_start: 0.4953 (OUTLIER) cc_final: 0.4669 (p90) REVERT: K 253 MET cc_start: 0.8152 (mtp) cc_final: 0.7735 (mmp) REVERT: K 294 LEU cc_start: 0.6359 (tp) cc_final: 0.5186 (tp) REVERT: F 88 TYR cc_start: 0.9092 (m-80) cc_final: 0.8798 (m-80) REVERT: H 32 GLU cc_start: 0.7922 (pt0) cc_final: 0.7711 (tt0) REVERT: H 34 TYR cc_start: 0.8679 (m-80) cc_final: 0.8377 (m-80) outliers start: 9 outliers final: 6 residues processed: 144 average time/residue: 0.1298 time to fit residues: 27.3685 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 135 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain H residue 60 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 44 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 51 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 chunk 126 optimal weight: 40.0000 chunk 28 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 112 optimal weight: 40.0000 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 39 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.110803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.073736 restraints weight = 38483.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.075537 restraints weight = 20853.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076719 restraints weight = 14845.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.077388 restraints weight = 12423.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077674 restraints weight = 11341.417| |-----------------------------------------------------------------------------| r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3157 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3157 r_free = 0.3157 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3157 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8345 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15751 Z= 0.153 Angle : 0.589 10.032 22623 Z= 0.351 Chirality : 0.042 0.267 2548 Planarity : 0.004 0.047 1763 Dihedral : 29.746 170.839 4680 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.01 % Favored : 94.99 % Rotamer: Outliers : 1.04 % Allowed : 10.62 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.27), residues: 1019 helix: 2.12 (0.22), residues: 591 sheet: -2.64 (0.94), residues: 26 loop : -2.09 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 187 TYR 0.022 0.001 TYR F 88 PHE 0.009 0.001 PHE H 62 TRP 0.005 0.001 TRP K 218 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.15 (15749) covalent geometry : angle 0.58914 / 0.35 (22623) hydrogen bonds : bond 0.05902 / 3.99 ( 756) hydrogen bonds : angle 3.43690 / 2.43 ( 1918) metal coordination : bond 0.00088 / 0.04 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 143 time to evaluate : 0.399 Fit side-chains REVERT: K 100 MET cc_start: 0.7022 (pmm) cc_final: 0.6765 (pmm) REVERT: K 218 TRP cc_start: 0.4932 (OUTLIER) cc_final: 0.4651 (p90) REVERT: K 253 MET cc_start: 0.8255 (mtp) cc_final: 0.7829 (mmp) REVERT: K 294 LEU cc_start: 0.6326 (tp) cc_final: 0.5123 (tp) REVERT: A 113 HIS cc_start: 0.8023 (OUTLIER) cc_final: 0.7646 (m170) REVERT: D 44 GLN cc_start: 0.8775 (tm-30) cc_final: 0.8558 (tm-30) REVERT: F 88 TYR cc_start: 0.9059 (m-10) cc_final: 0.8583 (m-80) REVERT: H 32 GLU cc_start: 0.7891 (pt0) cc_final: 0.7671 (tt0) REVERT: H 34 TYR cc_start: 0.8624 (m-80) cc_final: 0.8334 (m-80) outliers start: 9 outliers final: 6 residues processed: 148 average time/residue: 0.1310 time to fit residues: 28.3883 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 137 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain H residue 60 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 118 optimal weight: 40.0000 chunk 41 optimal weight: 9.9990 chunk 59 optimal weight: 9.9990 chunk 112 optimal weight: 40.0000 chunk 47 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 chunk 114 optimal weight: 40.0000 chunk 86 optimal weight: 4.9990 chunk 44 optimal weight: 0.6980 chunk 101 optimal weight: 50.0000 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.110259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073129 restraints weight = 38020.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074936 restraints weight = 20633.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 72)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076115 restraints weight = 14701.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076746 restraints weight = 12300.656| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076986 restraints weight = 11252.529| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15751 Z= 0.166 Angle : 0.596 8.027 22623 Z= 0.351 Chirality : 0.042 0.266 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.739 169.918 4680 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.54 % Allowed : 11.55 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.27), residues: 1019 helix: 2.09 (0.22), residues: 590 sheet: -2.64 (0.93), residues: 26 loop : -2.19 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 352 TYR 0.033 0.002 TYR C 57 PHE 0.011 0.001 PHE K 311 TRP 0.005 0.001 TRP K 218 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00312 / 0.17 (15749) covalent geometry : angle 0.59648 / 0.35 (22623) hydrogen bonds : bond 0.06107 / 4.11 ( 756) hydrogen bonds : angle 3.41446 / 2.41 ( 1918) metal coordination : bond 0.00121 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 140 time to evaluate : 0.386 Fit side-chains REVERT: K 100 MET cc_start: 0.7007 (pmm) cc_final: 0.6655 (pmm) REVERT: K 218 TRP cc_start: 0.4951 (OUTLIER) cc_final: 0.4663 (p90) REVERT: K 253 MET cc_start: 0.8324 (mtp) cc_final: 0.7763 (mmp) REVERT: K 294 LEU cc_start: 0.6353 (tp) cc_final: 0.5133 (tp) REVERT: K 307 TYR cc_start: 0.7136 (m-80) cc_final: 0.6345 (m-80) REVERT: A 113 HIS cc_start: 0.8199 (OUTLIER) cc_final: 0.7757 (m170) REVERT: D 97 LEU cc_start: 0.9248 (OUTLIER) cc_final: 0.8832 (mp) REVERT: H 46 HIS cc_start: 0.7748 (OUTLIER) cc_final: 0.7224 (m-70) outliers start: 22 outliers final: 11 residues processed: 156 average time/residue: 0.1239 time to fit residues: 28.5783 Evaluate side-chains 152 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 137 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 158 THR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 46 HIS Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.9990 chunk 66 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 4 optimal weight: 9.9990 chunk 95 optimal weight: 10.0000 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 0.0270 chunk 71 optimal weight: 1.9990 overall best weight: 1.8046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 46 HIS H 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.111041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.074734 restraints weight = 38331.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.076782 restraints weight = 21531.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.078396 restraints weight = 13727.053| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078165 restraints weight = 12455.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078188 restraints weight = 11707.150| |-----------------------------------------------------------------------------| r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3162 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3162 r_free = 0.3162 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3162 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 15751 Z= 0.144 Angle : 0.587 9.391 22623 Z= 0.347 Chirality : 0.041 0.264 2548 Planarity : 0.004 0.052 1763 Dihedral : 29.696 170.082 4680 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 1.62 % Allowed : 13.39 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.27), residues: 1019 helix: 2.30 (0.22), residues: 586 sheet: -2.58 (0.94), residues: 26 loop : -2.09 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 187 TYR 0.013 0.001 TYR F 88 PHE 0.011 0.001 PHE K 311 TRP 0.004 0.001 TRP K 218 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00243 / 0.14 (15749) covalent geometry : angle 0.58657 / 0.35 (22623) hydrogen bonds : bond 0.05472 / 3.68 ( 756) hydrogen bonds : angle 3.30803 / 2.35 ( 1918) metal coordination : bond 0.00066 / 0.03 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 142 time to evaluate : 0.421 Fit side-chains REVERT: K 100 MET cc_start: 0.7030 (pmm) cc_final: 0.6784 (pmm) REVERT: K 218 TRP cc_start: 0.4995 (OUTLIER) cc_final: 0.4665 (p90) REVERT: K 253 MET cc_start: 0.8470 (mtp) cc_final: 0.7863 (mmt) REVERT: K 294 LEU cc_start: 0.6499 (tp) cc_final: 0.5300 (tp) REVERT: A 113 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7634 (m170) REVERT: D 97 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8875 (mp) REVERT: F 88 TYR cc_start: 0.9044 (m-10) cc_final: 0.8590 (m-80) REVERT: H 32 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7631 (tt0) outliers start: 14 outliers final: 8 residues processed: 147 average time/residue: 0.1183 time to fit residues: 25.8808 Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 136 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 218 TRP Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 10 optimal weight: 30.0000 chunk 19 optimal weight: 0.7980 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.8980 chunk 6 optimal weight: 40.0000 chunk 39 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 181 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.112043 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.075538 restraints weight = 37971.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077352 restraints weight = 20333.997| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 64)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.078529 restraints weight = 14402.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 63)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079223 restraints weight = 11971.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.079519 restraints weight = 10891.243| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3195 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3195 r_free = 0.3195 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3195 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 15751 Z= 0.137 Angle : 0.562 9.055 22623 Z= 0.335 Chirality : 0.040 0.263 2548 Planarity : 0.004 0.058 1763 Dihedral : 29.656 170.162 4680 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer: Outliers : 1.85 % Allowed : 14.09 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.27), residues: 1019 helix: 2.41 (0.22), residues: 586 sheet: -2.54 (0.93), residues: 26 loop : -2.09 (0.27), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG K 352 TYR 0.009 0.001 TYR C 57 PHE 0.007 0.001 PHE B 61 TRP 0.004 0.001 TRP K 218 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.14 (15749) covalent geometry : angle 0.56213 / 0.33 (22623) hydrogen bonds : bond 0.04987 / 3.33 ( 756) hydrogen bonds : angle 3.15900 / 2.24 ( 1918) metal coordination : bond 0.00052 / 0.02 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.338 Fit side-chains REVERT: K 100 MET cc_start: 0.6978 (pmm) cc_final: 0.6738 (pmm) REVERT: K 253 MET cc_start: 0.8288 (mtp) cc_final: 0.7898 (mmp) REVERT: K 294 LEU cc_start: 0.6284 (tp) cc_final: 0.5072 (tp) REVERT: A 113 HIS cc_start: 0.8017 (OUTLIER) cc_final: 0.7599 (m170) REVERT: D 44 GLN cc_start: 0.8812 (tm-30) cc_final: 0.8601 (tm-30) REVERT: D 97 LEU cc_start: 0.9213 (OUTLIER) cc_final: 0.8888 (mp) REVERT: H 32 GLU cc_start: 0.7844 (pt0) cc_final: 0.7582 (tt0) outliers start: 16 outliers final: 10 residues processed: 153 average time/residue: 0.1182 time to fit residues: 26.8304 Evaluate side-chains 149 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 137 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 32 optimal weight: 5.9990 chunk 117 optimal weight: 50.0000 chunk 55 optimal weight: 0.4980 chunk 38 optimal weight: 4.9990 chunk 96 optimal weight: 0.5980 chunk 107 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 119 optimal weight: 30.0000 chunk 125 optimal weight: 30.0000 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.110686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.073922 restraints weight = 38044.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.075719 restraints weight = 20756.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.076792 restraints weight = 14696.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.077479 restraints weight = 12279.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077785 restraints weight = 11194.084| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3158 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3158 r_free = 0.3158 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15751 Z= 0.163 Angle : 0.593 9.785 22623 Z= 0.346 Chirality : 0.041 0.264 2548 Planarity : 0.004 0.059 1763 Dihedral : 29.717 169.621 4678 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.08 % Allowed : 14.32 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.27), residues: 1019 helix: 2.31 (0.22), residues: 588 sheet: -2.39 (0.94), residues: 26 loop : -2.14 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 187 TYR 0.010 0.001 TYR C 57 PHE 0.011 0.001 PHE K 311 TRP 0.012 0.003 TRP K 218 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.16 (15749) covalent geometry : angle 0.59316 / 0.35 (22623) hydrogen bonds : bond 0.05631 / 3.78 ( 756) hydrogen bonds : angle 3.25410 / 2.32 ( 1918) metal coordination : bond 0.00115 / 0.06 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.442 Fit side-chains REVERT: K 100 MET cc_start: 0.7004 (pmm) cc_final: 0.6604 (pmm) REVERT: K 253 MET cc_start: 0.8255 (mtp) cc_final: 0.7811 (mmp) REVERT: A 40 ARG cc_start: 0.6822 (mtm-85) cc_final: 0.6595 (mtm-85) REVERT: A 113 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7704 (m170) outliers start: 18 outliers final: 13 residues processed: 151 average time/residue: 0.1252 time to fit residues: 27.9965 Evaluate side-chains 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 140 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 96 optimal weight: 6.9990 chunk 41 optimal weight: 2.9990 chunk 116 optimal weight: 50.0000 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 30 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 131 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 115 optimal weight: 40.0000 chunk 98 optimal weight: 1.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.111018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.073857 restraints weight = 38484.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.075697 restraints weight = 20654.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.076939 restraints weight = 14599.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.077621 restraints weight = 12119.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.077916 restraints weight = 11037.723| |-----------------------------------------------------------------------------| r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8334 moved from start: 0.1655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15751 Z= 0.151 Angle : 0.586 9.947 22623 Z= 0.344 Chirality : 0.040 0.260 2548 Planarity : 0.004 0.057 1763 Dihedral : 29.713 169.645 4678 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.73 % Allowed : 15.13 % Favored : 83.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.27), residues: 1019 helix: 2.34 (0.22), residues: 588 sheet: -2.29 (0.94), residues: 26 loop : -2.16 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG K 352 TYR 0.012 0.001 TYR H 80 PHE 0.008 0.001 PHE K 311 TRP 0.008 0.002 TRP K 218 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (15749) covalent geometry : angle 0.58614 / 0.34 (22623) hydrogen bonds : bond 0.05417 / 3.63 ( 756) hydrogen bonds : angle 3.20371 / 2.29 ( 1918) metal coordination : bond 0.00102 / 0.05 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 140 time to evaluate : 0.436 Fit side-chains REVERT: K 100 MET cc_start: 0.7068 (pmm) cc_final: 0.6780 (pmm) REVERT: K 253 MET cc_start: 0.8321 (mtp) cc_final: 0.7877 (mmt) REVERT: K 307 TYR cc_start: 0.7280 (m-80) cc_final: 0.6400 (m-80) REVERT: A 40 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.6563 (mtm-85) REVERT: A 113 HIS cc_start: 0.8057 (OUTLIER) cc_final: 0.7653 (m170) REVERT: H 32 GLU cc_start: 0.7941 (pt0) cc_final: 0.7654 (tt0) outliers start: 15 outliers final: 13 residues processed: 149 average time/residue: 0.1152 time to fit residues: 25.5546 Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 136 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 5.9990 chunk 126 optimal weight: 30.0000 chunk 36 optimal weight: 8.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.0070 chunk 2 optimal weight: 7.9990 chunk 7 optimal weight: 7.9990 chunk 89 optimal weight: 9.9990 chunk 88 optimal weight: 3.9990 chunk 1 optimal weight: 9.9990 chunk 5 optimal weight: 6.9990 overall best weight: 3.5804 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.110284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.073118 restraints weight = 38229.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074946 restraints weight = 20170.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.076168 restraints weight = 14136.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.076877 restraints weight = 11691.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.077246 restraints weight = 10607.272| |-----------------------------------------------------------------------------| r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3144 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3144 r_free = 0.3144 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3144 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15751 Z= 0.171 Angle : 0.606 9.338 22623 Z= 0.352 Chirality : 0.041 0.257 2548 Planarity : 0.004 0.057 1763 Dihedral : 29.752 169.445 4678 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 1.85 % Allowed : 15.13 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.27), residues: 1019 helix: 2.25 (0.22), residues: 588 sheet: -2.34 (0.96), residues: 26 loop : -2.24 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 187 TYR 0.022 0.001 TYR F 88 PHE 0.010 0.001 PHE K 311 TRP 0.010 0.002 TRP K 218 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (15749) covalent geometry : angle 0.60570 / 0.35 (22623) hydrogen bonds : bond 0.05950 / 4.00 ( 756) hydrogen bonds : angle 3.28134 / 2.34 ( 1918) metal coordination : bond 0.00146 / 0.07 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 139 time to evaluate : 0.410 Fit side-chains REVERT: K 253 MET cc_start: 0.8295 (mtp) cc_final: 0.7802 (mmp) REVERT: A 40 ARG cc_start: 0.6892 (mtm-85) cc_final: 0.6658 (mtm-85) REVERT: A 113 HIS cc_start: 0.8194 (OUTLIER) cc_final: 0.7747 (m170) outliers start: 16 outliers final: 13 residues processed: 150 average time/residue: 0.1110 time to fit residues: 24.6817 Evaluate side-chains 151 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 137 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 91 optimal weight: 8.9990 chunk 123 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 70 optimal weight: 6.9990 chunk 56 optimal weight: 8.9990 chunk 42 optimal weight: 0.9990 chunk 115 optimal weight: 40.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.108181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.070772 restraints weight = 38312.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.072492 restraints weight = 21114.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.073622 restraints weight = 15184.645| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.074147 restraints weight = 12768.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 58)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.074590 restraints weight = 11763.992| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.072 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8405 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 15751 Z= 0.216 Angle : 0.672 10.963 22623 Z= 0.382 Chirality : 0.044 0.252 2548 Planarity : 0.005 0.057 1763 Dihedral : 29.867 168.680 4678 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 1.62 % Allowed : 15.82 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1019 helix: 1.92 (0.21), residues: 591 sheet: -2.41 (0.93), residues: 26 loop : -2.35 (0.27), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 32 TYR 0.021 0.002 TYR F 88 PHE 0.013 0.001 PHE K 311 TRP 0.015 0.003 TRP K 218 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.22 (15749) covalent geometry : angle 0.67244 / 0.38 (22623) hydrogen bonds : bond 0.07145 / 4.82 ( 756) hydrogen bonds : angle 3.52174 / 2.52 ( 1918) metal coordination : bond 0.00248 / 0.13 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2038 Ramachandran restraints generated. 1019 Oldfield, 0 Emsley, 1019 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.334 Fit side-chains REVERT: A 113 HIS cc_start: 0.8294 (OUTLIER) cc_final: 0.7834 (m170) REVERT: H 32 GLU cc_start: 0.8054 (pt0) cc_final: 0.7673 (tt0) outliers start: 14 outliers final: 13 residues processed: 146 average time/residue: 0.1165 time to fit residues: 24.9345 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 185 TYR Chi-restraints excluded: chain K residue 203 TYR Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 99 ARG Chi-restraints excluded: chain D residue 116 THR Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain H residue 108 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 35 optimal weight: 7.9990 chunk 96 optimal weight: 8.9990 chunk 127 optimal weight: 30.0000 chunk 117 optimal weight: 50.0000 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 9.9990 chunk 51 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 131 optimal weight: 40.0000 chunk 67 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.108463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.071005 restraints weight = 37949.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.072771 restraints weight = 20992.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 61)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.073906 restraints weight = 15078.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074555 restraints weight = 12659.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.074802 restraints weight = 11587.715| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.1845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15751 Z= 0.208 Angle : 0.661 8.648 22623 Z= 0.377 Chirality : 0.044 0.250 2548 Planarity : 0.004 0.056 1763 Dihedral : 29.885 169.160 4678 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 1.62 % Allowed : 16.28 % Favored : 82.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.26), residues: 1019 helix: 1.97 (0.21), residues: 586 sheet: -2.43 (0.95), residues: 26 loop : -2.37 (0.26), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 40 TYR 0.023 0.002 TYR F 88 PHE 0.012 0.001 PHE K 250 TRP 0.008 0.002 TRP K 218 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.21 (15749) covalent geometry : angle 0.66076 / 0.38 (22623) hydrogen bonds : bond 0.06872 / 4.63 ( 756) hydrogen bonds : angle 3.49053 / 2.49 ( 1918) metal coordination : bond 0.00228 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2931.96 seconds wall clock time: 50 minutes 55.04 seconds (3055.04 seconds total)