Starting phenix.real_space_refine on Fri Jul 3 19:26:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jhg_36265/07_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.cif" model { file = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jhg_36265/07_2026/8jhg_36265.map" } 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-dev-6108/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: 3.78, per 1000 atoms: 0.25 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: 1.47 Conformation dependent library (CDL) restraints added in 577.1 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: 2.99 Time building geometry restraints manager: 1.93 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: 21627 1.83 - 3.66: 943 3.66 - 5.49: 41 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: 1.010 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 18.970 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.920 ------------------------------------------------------------------------------- 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 : 0.737 9.152 22623 Z= 0.625 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 0.73732 / 0.62 (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 : 0.415 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: 0.1369 time to fit residues: 33.1414 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 : 0.427 ------------------------------------------------------------------------------- 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: 40.0000 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: 0.6980 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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 = 0.3799 r_free = 0.3799 target = 0.110876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.074160 restraints weight = 38232.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.076058 restraints weight = 20213.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 60)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.077291 restraints weight = 14160.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.077978 restraints weight = 11723.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3200 r_free = 0.3200 target = 0.078239 restraints weight = 10665.117| |-----------------------------------------------------------------------------| r_work (final): 0.3160 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3160 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3160 r_free = 0.3160 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 = 0.3160 r_free = 0.3160 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: 0.3160 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8338 moved from start: 0.0858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15751 Z= 0.169 Angle : 0.626 8.667 22623 Z= 0.371 Chirality : 0.043 0.248 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.737 169.713 4680 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.60 % Favored : 94.40 % Rotamer: Outliers : 1.04 % Allowed : 9.24 % Favored : 89.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.59 (0.27), residues: 1019 helix: 2.11 (0.22), residues: 582 sheet: -2.60 (0.94), residues: 26 loop : -2.10 (0.27), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 352 TYR 0.031 0.001 TYR F 88 PHE 0.010 0.001 PHE K 311 TRP 0.006 0.001 TRP K 218 HIS 0.005 0.001 HIS K 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.17 (15749) covalent geometry : angle 0.62554 / 0.37 (22623) hydrogen bonds : bond 0.06464 / 4.36 ( 756) hydrogen bonds : angle 3.62709 / 2.57 ( 1918) metal coordination : bond 0.00145 / 0.08 ( 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 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 141 time to evaluate : 0.522 Fit side-chains REVERT: K 100 MET cc_start: 0.7103 (pmm) cc_final: 0.6656 (pmm) REVERT: K 218 TRP cc_start: 0.4963 (OUTLIER) cc_final: 0.4681 (p90) REVERT: K 253 MET cc_start: 0.8198 (mtp) cc_final: 0.7830 (mmp) REVERT: K 294 LEU cc_start: 0.6344 (tp) cc_final: 0.5156 (tp) REVERT: F 88 TYR cc_start: 0.9077 (m-80) cc_final: 0.8726 (m-80) REVERT: H 34 TYR cc_start: 0.8676 (m-80) cc_final: 0.8368 (m-80) outliers start: 9 outliers final: 5 residues processed: 146 average time/residue: 0.1239 time to fit residues: 26.6419 Evaluate side-chains 142 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 136 time to evaluate : 0.402 ------------------------------------------------------------------------------- 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 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: 0.2980 chunk 21 optimal weight: 0.2980 chunk 51 optimal weight: 8.9990 chunk 55 optimal weight: 0.9990 chunk 126 optimal weight: 40.0000 chunk 28 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 112 optimal weight: 40.0000 chunk 36 optimal weight: 0.9980 chunk 5 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- 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 = 0.3825 r_free = 0.3825 target = 0.112295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.075991 restraints weight = 38423.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.077850 restraints weight = 20471.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.078976 restraints weight = 14314.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.079671 restraints weight = 11877.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.079971 restraints weight = 10813.379| |-----------------------------------------------------------------------------| r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3201 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3201 r_free = 0.3201 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3201 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 15751 Z= 0.140 Angle : 0.563 10.224 22623 Z= 0.341 Chirality : 0.040 0.248 2548 Planarity : 0.004 0.047 1763 Dihedral : 29.716 170.422 4680 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.92 % Allowed : 10.51 % Favored : 88.57 % 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: 0.85 (0.27), residues: 1019 helix: 2.34 (0.22), residues: 584 sheet: -2.60 (0.94), residues: 26 loop : -2.01 (0.27), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 352 TYR 0.023 0.001 TYR F 88 PHE 0.013 0.001 PHE H 62 TRP 0.005 0.001 TRP K 218 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.14 (15749) covalent geometry : angle 0.56340 / 0.34 (22623) hydrogen bonds : bond 0.05250 / 3.54 ( 756) hydrogen bonds : angle 3.33544 / 2.36 ( 1918) metal coordination : bond 0.00024 / 0.01 ( 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 154 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 146 time to evaluate : 0.405 Fit side-chains REVERT: K 100 MET cc_start: 0.6990 (pmm) cc_final: 0.6727 (pmm) REVERT: K 218 TRP cc_start: 0.4883 (OUTLIER) cc_final: 0.4492 (p90) REVERT: K 253 MET cc_start: 0.8196 (mtp) cc_final: 0.7800 (mmp) REVERT: K 294 LEU cc_start: 0.6248 (tp) cc_final: 0.4983 (tp) REVERT: A 99 TYR cc_start: 0.8480 (t80) cc_final: 0.8239 (t80) REVERT: D 44 GLN cc_start: 0.8792 (tm-30) cc_final: 0.8586 (tm-30) REVERT: F 88 TYR cc_start: 0.9004 (m-10) cc_final: 0.8493 (m-80) REVERT: H 46 HIS cc_start: 0.7552 (OUTLIER) cc_final: 0.7049 (m-70) outliers start: 8 outliers final: 5 residues processed: 149 average time/residue: 0.1259 time to fit residues: 27.7506 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 139 time to evaluate : 0.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 72 MET 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 B residue 30 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 46 HIS 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: 10.0000 chunk 59 optimal weight: 0.0570 chunk 112 optimal weight: 40.0000 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 16 optimal weight: 20.0000 chunk 114 optimal weight: 40.0000 chunk 86 optimal weight: 3.9990 chunk 44 optimal weight: 0.1980 chunk 101 optimal weight: 50.0000 overall best weight: 1.1500 ------------------------------------------------------------------------------- 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 = 0.3829 r_free = 0.3829 target = 0.112537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.076149 restraints weight = 38294.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078003 restraints weight = 20407.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.079192 restraints weight = 14366.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 49)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.079889 restraints weight = 11940.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.080177 restraints weight = 10879.162| |-----------------------------------------------------------------------------| r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3204 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3204 r_free = 0.3204 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3204 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8290 moved from start: 0.1336 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= 0.135 Angle : 0.550 7.798 22623 Z= 0.332 Chirality : 0.040 0.253 2548 Planarity : 0.004 0.054 1763 Dihedral : 29.665 169.850 4680 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 1.27 % Allowed : 11.78 % Favored : 86.95 % 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: 0.98 (0.27), residues: 1019 helix: 2.48 (0.22), residues: 581 sheet: -2.56 (0.94), residues: 26 loop : -2.01 (0.26), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.015 0.001 TYR F 88 PHE 0.010 0.001 PHE K 311 TRP 0.005 0.001 TRP K 218 HIS 0.012 0.001 HIS H 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00209 / 0.13 (15749) covalent geometry : angle 0.55000 / 0.33 (22623) hydrogen bonds : bond 0.04993 / 3.34 ( 756) hydrogen bonds : angle 3.22414 / 2.28 ( 1918) metal coordination : bond 0.00031 / 0.01 ( 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 158 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 147 time to evaluate : 0.411 Fit side-chains REVERT: K 100 MET cc_start: 0.6905 (pmm) cc_final: 0.6630 (pmm) REVERT: K 218 TRP cc_start: 0.4949 (OUTLIER) cc_final: 0.4586 (p90) REVERT: K 253 MET cc_start: 0.8304 (mtp) cc_final: 0.7835 (mmt) REVERT: K 294 LEU cc_start: 0.6235 (tp) cc_final: 0.4964 (tp) REVERT: K 307 TYR cc_start: 0.7231 (m-80) cc_final: 0.6530 (m-80) REVERT: A 113 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7705 (m170) REVERT: F 88 TYR cc_start: 0.9043 (m-10) cc_final: 0.8528 (m-80) outliers start: 11 outliers final: 6 residues processed: 153 average time/residue: 0.1229 time to fit residues: 27.8032 Evaluate side-chains 147 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 139 time to evaluate : 0.373 ------------------------------------------------------------------------------- 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 E residue 112 ILE Chi-restraints excluded: chain H residue 60 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 30 optimal weight: 0.4980 chunk 66 optimal weight: 5.9990 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 86 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 95 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 10 optimal weight: 30.0000 chunk 71 optimal weight: 4.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- 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 = 0.3813 r_free = 0.3813 target = 0.111444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074542 restraints weight = 38410.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076414 restraints weight = 20435.466| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3193 r_free = 0.3193 target = 0.077521 restraints weight = 14282.197| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.078206 restraints weight = 11848.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.078539 restraints weight = 10779.431| |-----------------------------------------------------------------------------| r_work (final): 0.3172 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3172 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3172 r_free = 0.3172 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 = 0.3172 r_free = 0.3172 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: 0.3172 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15751 Z= 0.157 Angle : 0.576 10.401 22623 Z= 0.343 Chirality : 0.040 0.255 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.699 169.024 4680 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 2.31 % Allowed : 11.66 % Favored : 86.03 % 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: 0.86 (0.27), residues: 1019 helix: 2.34 (0.22), residues: 588 sheet: -2.58 (0.93), residues: 26 loop : -2.04 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 187 TYR 0.028 0.001 TYR C 57 PHE 0.009 0.001 PHE K 311 TRP 0.005 0.001 TRP K 218 HIS 0.005 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00290 / 0.16 (15749) covalent geometry : angle 0.57650 / 0.34 (22623) hydrogen bonds : bond 0.05503 / 3.70 ( 756) hydrogen bonds : angle 3.29419 / 2.34 ( 1918) metal coordination : bond 0.00086 / 0.04 ( 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 162 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 142 time to evaluate : 0.414 Fit side-chains REVERT: K 100 MET cc_start: 0.6938 (pmm) cc_final: 0.6457 (pmm) REVERT: K 218 TRP cc_start: 0.4945 (OUTLIER) cc_final: 0.4655 (p90) REVERT: K 253 MET cc_start: 0.8333 (mtp) cc_final: 0.7876 (mmp) REVERT: K 294 LEU cc_start: 0.6298 (tp) cc_final: 0.5082 (tp) REVERT: A 113 HIS cc_start: 0.8112 (OUTLIER) cc_final: 0.7728 (m170) outliers start: 20 outliers final: 10 residues processed: 153 average time/residue: 0.1235 time to fit residues: 28.0456 Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 138 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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 260 CYS 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 C residue 111 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 43 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 8.9990 chunk 79 optimal weight: 0.9980 chunk 47 optimal weight: 0.7980 chunk 59 optimal weight: 6.9990 chunk 10 optimal weight: 20.0000 chunk 19 optimal weight: 0.8980 chunk 96 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 6 optimal weight: 40.0000 chunk 39 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- 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 = 0.3836 r_free = 0.3836 target = 0.112903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.076269 restraints weight = 38493.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 62)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.078150 restraints weight = 20837.410| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.079360 restraints weight = 14759.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.079939 restraints weight = 12301.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.080396 restraints weight = 11266.884| |-----------------------------------------------------------------------------| r_work (final): 0.3210 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3209 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3209 r_free = 0.3209 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3209 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15751 Z= 0.133 Angle : 0.550 9.846 22623 Z= 0.330 Chirality : 0.039 0.252 2548 Planarity : 0.004 0.054 1763 Dihedral : 29.630 169.221 4680 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.50 % Allowed : 13.51 % 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: 1.03 (0.27), residues: 1019 helix: 2.50 (0.22), residues: 587 sheet: -2.51 (0.94), residues: 26 loop : -2.00 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 128 TYR 0.017 0.001 TYR H 80 PHE 0.006 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 0.00213 / 0.13 (15749) covalent geometry : angle 0.54970 / 0.33 (22623) hydrogen bonds : bond 0.04684 / 3.12 ( 756) hydrogen bonds : angle 3.10372 / 2.21 ( 1918) metal coordination : bond 0.00059 / 0.03 ( 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 155 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.350 Fit side-chains REVERT: K 100 MET cc_start: 0.6945 (pmm) cc_final: 0.6687 (pmm) REVERT: K 218 TRP cc_start: 0.4931 (OUTLIER) cc_final: 0.4704 (p90) REVERT: K 253 MET cc_start: 0.8268 (mtp) cc_final: 0.7903 (mmp) REVERT: K 294 LEU cc_start: 0.6284 (tp) cc_final: 0.5044 (tp) REVERT: A 113 HIS cc_start: 0.8007 (OUTLIER) cc_final: 0.7690 (m170) REVERT: F 88 TYR cc_start: 0.9015 (m-10) cc_final: 0.8647 (m-80) outliers start: 13 outliers final: 9 residues processed: 147 average time/residue: 0.1090 time to fit residues: 23.8918 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 134 time to evaluate : 0.505 ------------------------------------------------------------------------------- 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 260 CYS 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 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: 40.0000 chunk 55 optimal weight: 4.9990 chunk 38 optimal weight: 0.2980 chunk 96 optimal weight: 0.0030 chunk 107 optimal weight: 30.0000 chunk 92 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 23 optimal weight: 9.9990 chunk 119 optimal weight: 30.0000 chunk 125 optimal weight: 30.0000 overall best weight: 2.6596 ------------------------------------------------------------------------------- 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 = 0.3819 r_free = 0.3819 target = 0.111752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.074876 restraints weight = 38180.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 63)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.076817 restraints weight = 20064.984| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.078078 restraints weight = 13971.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 56)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.078768 restraints weight = 11532.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.078945 restraints weight = 10469.649| |-----------------------------------------------------------------------------| r_work (final): 0.3179 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3179 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3179 r_free = 0.3179 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 = 0.3179 r_free = 0.3179 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: 0.3179 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15751 Z= 0.152 Angle : 0.572 10.213 22623 Z= 0.338 Chirality : 0.040 0.253 2548 Planarity : 0.004 0.055 1763 Dihedral : 29.688 168.915 4680 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.30 % Favored : 94.70 % Rotamer: Outliers : 1.85 % Allowed : 13.63 % Favored : 84.53 % 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: 0.99 (0.27), residues: 1019 helix: 2.46 (0.22), residues: 588 sheet: -2.45 (0.93), residues: 26 loop : -2.04 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 187 TYR 0.013 0.001 TYR H 80 PHE 0.011 0.001 PHE K 311 TRP 0.004 0.001 TRP K 218 HIS 0.004 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.15 (15749) covalent geometry : angle 0.57174 / 0.34 (22623) hydrogen bonds : bond 0.05311 / 3.55 ( 756) hydrogen bonds : angle 3.16852 / 2.26 ( 1918) metal coordination : bond 0.00100 / 0.05 ( 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 157 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 141 time to evaluate : 0.399 Fit side-chains REVERT: K 218 TRP cc_start: 0.4928 (OUTLIER) cc_final: 0.4723 (p90) REVERT: K 253 MET cc_start: 0.8320 (mtp) cc_final: 0.7897 (mmp) REVERT: K 294 LEU cc_start: 0.6367 (tp) cc_final: 0.5168 (tp) REVERT: A 113 HIS cc_start: 0.8052 (OUTLIER) cc_final: 0.7716 (m170) REVERT: H 34 TYR cc_start: 0.8705 (m-80) cc_final: 0.8428 (m-80) outliers start: 16 outliers final: 13 residues processed: 148 average time/residue: 0.1257 time to fit residues: 27.3216 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 : 0.425 ------------------------------------------------------------------------------- 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 218 TRP Chi-restraints excluded: chain K residue 260 CYS Chi-restraints excluded: chain K residue 265 LEU Chi-restraints excluded: chain K residue 297 ILE 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 E residue 112 ILE Chi-restraints excluded: chain E residue 122 LYS 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: 9.9990 chunk 41 optimal weight: 5.9990 chunk 116 optimal weight: 50.0000 chunk 57 optimal weight: 0.8980 chunk 73 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 9.9990 chunk 131 optimal weight: 50.0000 chunk 100 optimal weight: 50.0000 chunk 115 optimal weight: 50.0000 chunk 98 optimal weight: 3.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- 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 = 0.3811 r_free = 0.3811 target = 0.111226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.074373 restraints weight = 38469.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.076249 restraints weight = 20750.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 62)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.077444 restraints weight = 14676.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.078062 restraints weight = 12222.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.078352 restraints weight = 11159.950| |-----------------------------------------------------------------------------| r_work (final): 0.3168 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3170 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3170 r_free = 0.3170 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 = 0.3170 r_free = 0.3170 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: 0.3170 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1688 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= 0.155 Angle : 0.576 9.049 22623 Z= 0.339 Chirality : 0.040 0.249 2548 Planarity : 0.004 0.056 1763 Dihedral : 29.712 168.391 4680 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 1.73 % Allowed : 13.63 % Favored : 84.64 % 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: 0.92 (0.27), residues: 1019 helix: 2.43 (0.22), residues: 588 sheet: -2.28 (0.94), residues: 26 loop : -2.13 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 29 TYR 0.014 0.001 TYR H 80 PHE 0.009 0.001 PHE K 311 TRP 0.004 0.001 TRP K 218 HIS 0.003 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.15 (15749) covalent geometry : angle 0.57571 / 0.34 (22623) hydrogen bonds : bond 0.05459 / 3.66 ( 756) hydrogen bonds : angle 3.20149 / 2.28 ( 1918) metal coordination : bond 0.00110 / 0.06 ( 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 156 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 141 time to evaluate : 0.289 Fit side-chains REVERT: K 100 MET cc_start: 0.6930 (pmm) cc_final: 0.6682 (pmm) REVERT: K 218 TRP cc_start: 0.5008 (OUTLIER) cc_final: 0.4770 (p90) REVERT: K 253 MET cc_start: 0.8317 (mtp) cc_final: 0.7864 (mmp) REVERT: K 294 LEU cc_start: 0.6388 (tp) cc_final: 0.5246 (tp) REVERT: K 307 TYR cc_start: 0.7280 (m-80) cc_final: 0.6587 (m-80) REVERT: A 113 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7728 (m170) REVERT: H 34 TYR cc_start: 0.8696 (m-80) cc_final: 0.8451 (m-80) outliers start: 15 outliers final: 13 residues processed: 150 average time/residue: 0.1084 time to fit residues: 23.8908 Evaluate side-chains 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 135 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 218 TRP Chi-restraints excluded: chain K residue 260 CYS 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 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 108 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 87 optimal weight: 3.9990 chunk 126 optimal weight: 30.0000 chunk 36 optimal weight: 3.9990 chunk 59 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 2 optimal weight: 10.0000 chunk 7 optimal weight: 5.9990 chunk 89 optimal weight: 0.9980 chunk 88 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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 = 0.3818 r_free = 0.3818 target = 0.111726 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.075222 restraints weight = 38793.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.077062 restraints weight = 20819.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.078250 restraints weight = 14718.881| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.078880 restraints weight = 12242.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.079301 restraints weight = 11159.199| |-----------------------------------------------------------------------------| r_work (final): 0.3191 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3191 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3191 r_free = 0.3191 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 = 0.3191 r_free = 0.3191 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: 0.3191 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15751 Z= 0.138 Angle : 0.561 10.780 22623 Z= 0.333 Chirality : 0.039 0.245 2548 Planarity : 0.004 0.056 1763 Dihedral : 29.681 169.063 4680 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.50 % Allowed : 14.32 % Favored : 84.18 % 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: 1.02 (0.27), residues: 1019 helix: 2.52 (0.22), residues: 588 sheet: -2.27 (0.95), residues: 26 loop : -2.10 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.014 0.001 TYR F 88 PHE 0.008 0.001 PHE K 311 TRP 0.003 0.001 TRP K 218 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.14 (15749) covalent geometry : angle 0.56133 / 0.33 (22623) hydrogen bonds : bond 0.05016 / 3.34 ( 756) hydrogen bonds : angle 3.08679 / 2.21 ( 1918) metal coordination : bond 0.00082 / 0.04 ( 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 150 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 137 time to evaluate : 0.398 Fit side-chains REVERT: K 218 TRP cc_start: 0.4977 (OUTLIER) cc_final: 0.4765 (p90) REVERT: K 253 MET cc_start: 0.8322 (mtp) cc_final: 0.7886 (mmp) REVERT: K 294 LEU cc_start: 0.6454 (tp) cc_final: 0.5333 (tp) REVERT: A 113 HIS cc_start: 0.8040 (OUTLIER) cc_final: 0.7740 (m170) REVERT: H 34 TYR cc_start: 0.8665 (m-80) cc_final: 0.8401 (m-80) outliers start: 13 outliers final: 11 residues processed: 144 average time/residue: 0.1177 time to fit residues: 25.0649 Evaluate side-chains 145 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 132 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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 218 TRP Chi-restraints excluded: chain K residue 260 CYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 132 random chunks: chunk 91 optimal weight: 9.9990 chunk 123 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 116 optimal weight: 50.0000 chunk 3 optimal weight: 0.0670 chunk 54 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 70 optimal weight: 10.0000 chunk 56 optimal weight: 0.0010 chunk 42 optimal weight: 5.9990 chunk 115 optimal weight: 40.0000 overall best weight: 4.0130 ------------------------------------------------------------------------------- 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 = 0.110241 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.073113 restraints weight = 38051.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.074883 restraints weight = 20769.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.076047 restraints weight = 14859.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.076668 restraints weight = 12423.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.077049 restraints weight = 11344.243| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3140 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3140 r_free = 0.3140 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 = 0.3140 r_free = 0.3140 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: 0.3140 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15751 Z= 0.183 Angle : 0.613 8.809 22623 Z= 0.354 Chirality : 0.041 0.243 2548 Planarity : 0.004 0.058 1763 Dihedral : 29.763 168.148 4680 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 1.73 % Allowed : 14.32 % Favored : 83.95 % 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: 0.77 (0.27), residues: 1019 helix: 2.34 (0.22), residues: 588 sheet: -2.21 (0.97), residues: 26 loop : -2.25 (0.27), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 29 TYR 0.016 0.002 TYR F 88 PHE 0.013 0.001 PHE K 311 TRP 0.004 0.001 TRP K 218 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.18 (15749) covalent geometry : angle 0.61309 / 0.35 (22623) hydrogen bonds : bond 0.06164 / 4.14 ( 756) hydrogen bonds : angle 3.31102 / 2.37 ( 1918) metal coordination : bond 0.00162 / 0.08 ( 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: 15 poor density : 133 time to evaluate : 0.401 Fit side-chains REVERT: K 218 TRP cc_start: 0.5067 (OUTLIER) cc_final: 0.4812 (p90) REVERT: K 253 MET cc_start: 0.8329 (mtp) cc_final: 0.7786 (mmt) REVERT: K 294 LEU cc_start: 0.6490 (tp) cc_final: 0.5318 (tp) REVERT: K 307 TYR cc_start: 0.7169 (m-80) cc_final: 0.6506 (m-80) REVERT: A 113 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7828 (m170) outliers start: 15 outliers final: 12 residues processed: 145 average time/residue: 0.1071 time to fit residues: 23.3387 Evaluate side-chains 146 residues out of total 880 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 132 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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 218 TRP Chi-restraints excluded: chain K residue 260 CYS 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 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: 10.0000 chunk 96 optimal weight: 9.9990 chunk 127 optimal weight: 30.0000 chunk 117 optimal weight: 50.0000 chunk 47 optimal weight: 0.8980 chunk 44 optimal weight: 8.9990 chunk 51 optimal weight: 7.9990 chunk 16 optimal weight: 8.9990 chunk 131 optimal weight: 50.0000 chunk 67 optimal weight: 1.9990 chunk 6 optimal weight: 10.0000 overall best weight: 5.7788 ------------------------------------------------------------------------------- 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 = 0.3772 r_free = 0.3772 target = 0.108699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.071251 restraints weight = 37995.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.072994 restraints weight = 21019.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.073992 restraints weight = 15107.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.074717 restraints weight = 12809.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.074953 restraints weight = 11694.723| |-----------------------------------------------------------------------------| r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3102 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3102 r_free = 0.3102 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 = 0.3102 r_free = 0.3102 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: 0.3102 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1827 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= 0.224 Angle : 0.664 9.761 22623 Z= 0.377 Chirality : 0.043 0.239 2548 Planarity : 0.005 0.057 1763 Dihedral : 29.860 167.336 4680 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 1.62 % Allowed : 14.43 % Favored : 83.95 % 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: 0.38 (0.26), residues: 1019 helix: 1.97 (0.21), residues: 590 sheet: -2.29 (0.95), residues: 26 loop : -2.34 (0.27), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 29 TYR 0.019 0.002 TYR F 88 PHE 0.014 0.001 PHE A 104 TRP 0.005 0.002 TRP K 264 HIS 0.006 0.001 HIS D 46 Details of bonding type rmsd/Z covalent geometry : bond 0.00476 / 0.22 (15749) covalent geometry : angle 0.66353 / 0.38 (22623) hydrogen bonds : bond 0.07018 / 4.73 ( 756) hydrogen bonds : angle 3.48765 / 2.49 ( 1918) metal coordination : bond 0.00223 / 0.11 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2896.09 seconds wall clock time: 50 minutes 19.58 seconds (3019.58 seconds total)