Starting phenix.real_space_refine on Sat Sep 12 23:58:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.map" model { file = "/net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nog_0468/09_2026/6nog_0468.cif" } resolution = 3.9 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 5986 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: 5 Type Number sf(0) Gaussians P 292 5.49 5 S 27 5.16 5 C 8489 2.51 5 N 2751 2.21 5 O 3370 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14929 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "E" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 78, 619 Classifications: {'peptide': 78} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 76} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 800 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "D" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "L" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 593 Classifications: {'peptide': 74} Link IDs: {'PTRANS': 3, 'TRANS': 70} Chain: "K" Number of atoms: 2431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2431 Classifications: {'peptide': 302} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 288} Chain breaks: 3 Unresolved non-hydrogen bonds: 36 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 32 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 3.12, per 1000 atoms: 0.21 Number of scatterers: 14929 At special positions: 0 Unit cell: (118.104, 138.32, 118.104, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 P 292 15.00 O 3370 8.00 N 2751 7.00 C 8489 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: 1.13 Conformation dependent library (CDL) restraints added in 554.5 milliseconds 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2116 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 9 sheets defined 63.2% alpha, 5.5% beta 135 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.10 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 75 removed outlier: 3.843A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ALA A 75 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 78 No H-bonds generated for 'chain 'A' and resid 76 through 78' Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.700A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.913A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.925A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 113 removed outlier: 3.604A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 4.103A pdb=" N ILE E 130 " --> pdb=" O LEU E 126 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 removed outlier: 3.768A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.417A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 removed outlier: 4.095A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.586A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) removed outlier: 3.622A 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 50 through 75 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.820A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY F 94 " --> pdb=" O LEU F 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 removed outlier: 3.527A pdb=" N ARG C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 36 Processing helix chain 'C' and resid 46 through 72 removed outlier: 4.137A pdb=" N ASP C 72 " --> pdb=" O ASN C 68 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.635A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 removed outlier: 4.026A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.986A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.747A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL G 87 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG G 88 " --> pdb=" O GLN G 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.524A pdb=" N ASN G 94 " --> pdb=" O ASP G 90 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 46 removed outlier: 3.783A pdb=" N VAL D 41 " --> pdb=" O TYR D 37 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LYS D 46 " --> pdb=" O TYR D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 55 through 83 removed outlier: 3.653A pdb=" N SER D 60 " --> pdb=" O SER D 56 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N LEU D 80 " --> pdb=" O GLU D 76 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA D 81 " --> pdb=" O ALA D 77 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N HIS D 82 " --> pdb=" O SER D 78 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N TYR D 83 " --> pdb=" O ARG D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.504A pdb=" N ARG D 99 " --> pdb=" O GLN D 95 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU D 100 " --> pdb=" O THR D 96 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LEU D 101 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU D 102 " --> pdb=" O VAL D 98 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 122 removed outlier: 4.504A pdb=" N THR D 119 " --> pdb=" O THR D 115 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N CYS D 120 " --> pdb=" O LYS D 116 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N TYR D 121 " --> pdb=" O ALA D 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 46 removed outlier: 3.769A pdb=" N VAL H 41 " --> pdb=" O TYR H 37 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS H 46 " --> pdb=" O TYR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 55 through 83 removed outlier: 3.777A pdb=" N LEU H 80 " --> pdb=" O GLU H 76 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ALA H 81 " --> pdb=" O ALA H 77 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N HIS H 82 " --> pdb=" O SER H 78 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 102 removed outlier: 3.965A pdb=" N THR H 96 " --> pdb=" O ARG H 92 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU H 100 " --> pdb=" O THR H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 removed outlier: 3.848A pdb=" N CYS H 120 " --> pdb=" O LYS H 116 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N THR H 122 " --> pdb=" O VAL H 118 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 35 Processing helix chain 'L' and resid 37 through 39 No H-bonds generated for 'chain 'L' and resid 37 through 39' Processing helix chain 'L' and resid 55 through 60 removed outlier: 3.577A pdb=" N TYR L 59 " --> pdb=" O LEU L 56 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN L 60 " --> pdb=" O SER L 57 " (cutoff:3.500A) Processing helix chain 'K' and resid 33 through 48 Processing helix chain 'K' and resid 48 through 57 Processing helix chain 'K' and resid 67 through 91 Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 140 through 151 removed outlier: 3.518A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 Processing helix chain 'K' and resid 188 through 210 Processing helix chain 'K' and resid 225 through 234 removed outlier: 3.511A pdb=" N ARG K 229 " --> pdb=" O SER K 225 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG K 231 " --> pdb=" O GLU K 227 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 258 Processing helix chain 'K' and resid 286 through 289 Processing helix chain 'K' and resid 319 through 329 removed outlier: 3.544A pdb=" N GLU K 323 " --> pdb=" O ARG K 319 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.099A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.709A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.510A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'L' and resid 12 through 16 removed outlier: 3.512A pdb=" N LEU L 15 " --> pdb=" O ILE L 3 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N PHE L 45 " --> pdb=" O LYS L 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 6 through 9 removed outlier: 3.522A pdb=" N LEU K 7 " --> pdb=" O TYR K 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AA9, first strand: chain 'K' and resid 216 through 220 removed outlier: 6.225A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLU K 219 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 5.781A pdb=" N GLY K 184 " --> pdb=" O GLU K 219 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1407 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 350 hydrogen bonds 700 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.66 Time building geometry restraints manager: 1.58 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: 2744 1.33 - 1.45: 5049 1.45 - 1.57: 7375 1.57 - 1.69: 583 1.69 - 1.82: 47 Bond restraints: 15798 Sorted by residual: bond pdb=" C3' DT J 88 " pdb=" O3' DT J 88 " ideal model delta sigma weight residual 1.435 1.373 0.062 1.30e-02 5.92e+03 2.26e+01 bond pdb=" C3' DG I 122 " pdb=" O3' DG I 122 " ideal model delta sigma weight residual 1.435 1.375 0.060 1.30e-02 5.92e+03 2.15e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.435 1.495 -0.060 1.30e-02 5.92e+03 2.12e+01 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.435 1.494 -0.059 1.30e-02 5.92e+03 2.06e+01 bond pdb=" C3' DG I 102 " pdb=" O3' DG I 102 " ideal model delta sigma weight residual 1.435 1.376 0.059 1.30e-02 5.92e+03 2.04e+01 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 21429 2.48 - 4.97: 1066 4.97 - 7.45: 81 7.45 - 9.93: 21 9.93 - 12.41: 4 Bond angle restraints: 22601 Sorted by residual: angle pdb=" O4' DA I 91 " pdb=" C4' DA I 91 " pdb=" C3' DA I 91 " ideal model delta sigma weight residual 106.00 101.92 4.08 6.00e-01 2.78e+00 4.62e+01 angle pdb=" O4' DT I 48 " pdb=" C4' DT I 48 " pdb=" C3' DT I 48 " ideal model delta sigma weight residual 106.00 102.14 3.86 6.00e-01 2.78e+00 4.14e+01 angle pdb=" O4' DG J 56 " pdb=" C4' DG J 56 " pdb=" C3' DG J 56 " ideal model delta sigma weight residual 106.00 102.36 3.64 6.00e-01 2.78e+00 3.68e+01 angle pdb=" O4' DG J 137 " pdb=" C4' DG J 137 " pdb=" C3' DG J 137 " ideal model delta sigma weight residual 106.00 102.65 3.35 6.00e-01 2.78e+00 3.11e+01 angle pdb=" C ARG F 23 " pdb=" N ASP F 24 " pdb=" CA ASP F 24 " ideal model delta sigma weight residual 122.46 129.87 -7.41 1.41e+00 5.03e-01 2.76e+01 ... (remaining 22596 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.82: 7037 31.82 - 63.65: 1668 63.65 - 95.47: 50 95.47 - 127.29: 0 127.29 - 159.12: 3 Dihedral angle restraints: 8758 sinusoidal: 5489 harmonic: 3269 Sorted by residual: dihedral pdb=" CA ARG A 63 " pdb=" C ARG A 63 " pdb=" N LYS A 64 " pdb=" CA LYS A 64 " ideal model delta harmonic sigma weight residual -180.00 -151.77 -28.23 0 5.00e+00 4.00e-02 3.19e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual 180.00 -155.74 -24.26 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 -157.19 -22.81 0 5.00e+00 4.00e-02 2.08e+01 ... (remaining 8755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1909 0.071 - 0.142: 568 0.142 - 0.213: 71 0.213 - 0.284: 13 0.284 - 0.355: 8 Chirality restraints: 2569 Sorted by residual: chirality pdb=" CG LEU K 107 " pdb=" CB LEU K 107 " pdb=" CD1 LEU K 107 " pdb=" CD2 LEU K 107 " both_signs ideal model delta sigma weight residual False -2.59 -2.94 0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CB ILE K 151 " pdb=" CA ILE K 151 " pdb=" CG1 ILE K 151 " pdb=" CG2 ILE K 151 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.33 2.00e-01 2.50e+01 2.73e+00 chirality pdb=" CA LEU K 299 " pdb=" N LEU K 299 " pdb=" C LEU K 299 " pdb=" CB LEU K 299 " both_signs ideal model delta sigma weight residual False 2.51 2.84 -0.33 2.00e-01 2.50e+01 2.68e+00 ... (remaining 2566 not shown) Planarity restraints: 1855 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU H 102 " -0.048 5.00e-02 4.00e+02 7.15e-02 8.19e+00 pdb=" N PRO H 103 " 0.124 5.00e-02 4.00e+02 pdb=" CA PRO H 103 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO H 103 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE K 266 " 0.013 2.00e-02 2.50e+03 2.70e-02 7.31e+00 pdb=" C ILE K 266 " -0.047 2.00e-02 2.50e+03 pdb=" O ILE K 266 " 0.018 2.00e-02 2.50e+03 pdb=" N VAL K 267 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 91 " -0.036 2.00e-02 2.50e+03 1.59e-02 6.96e+00 pdb=" N9 DA I 91 " 0.030 2.00e-02 2.50e+03 pdb=" C8 DA I 91 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 91 " 0.011 2.00e-02 2.50e+03 pdb=" C5 DA I 91 " -0.009 2.00e-02 2.50e+03 pdb=" C6 DA I 91 " -0.005 2.00e-02 2.50e+03 pdb=" N6 DA I 91 " -0.012 2.00e-02 2.50e+03 pdb=" N1 DA I 91 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I 91 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DA I 91 " 0.009 2.00e-02 2.50e+03 pdb=" C4 DA I 91 " 0.009 2.00e-02 2.50e+03 ... (remaining 1852 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2724 2.77 - 3.30: 12860 3.30 - 3.84: 28212 3.84 - 4.37: 30410 4.37 - 4.90: 43971 Nonbonded interactions: 118177 Sorted by model distance: nonbonded pdb=" OG1 THR K 154 " pdb=" OD1 ASP K 155 " model vdw 2.239 3.040 nonbonded pdb=" O TYR G 39 " pdb=" OG SER H 78 " model vdw 2.274 3.040 nonbonded pdb=" O ASP K 161 " pdb=" OG SER K 164 " model vdw 2.293 3.040 nonbonded pdb=" O TYR C 39 " pdb=" OG SER D 78 " model vdw 2.302 3.040 nonbonded pdb=" OD1 ASN K 242 " pdb=" OG SER K 268 " model vdw 2.327 3.040 ... (remaining 118172 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' selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 14 through 117) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 32 through 124) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.290 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.000 Extract box with map and model: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 15.320 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 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 : 0.010 0.070 15798 Z= 0.810 Angle : 1.203 12.415 22601 Z= 0.900 Chirality : 0.067 0.355 2569 Planarity : 0.008 0.072 1855 Dihedral : 26.638 159.118 6642 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 0.84 % Allowed : 7.67 % Favored : 91.49 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.63 % 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: -1.83 (0.22), residues: 1098 helix: -1.16 (0.17), residues: 634 sheet: 0.01 (0.56), residues: 79 loop : -1.28 (0.31), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K 203 TYR 0.030 0.004 TYR K 27 PHE 0.032 0.004 PHE K 159 TRP 0.030 0.004 TRP K 208 HIS 0.008 0.003 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.01018 / 0.81 (15798) covalent geometry : angle 1.20253 / 0.90 (22601) hydrogen bonds : bond 0.15789 / 9.73 ( 830) hydrogen bonds : angle 5.31407 / 3.75 ( 2107) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 386 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8253 (mt) cc_final: 0.7951 (mt) REVERT: A 80 THR cc_start: 0.8161 (t) cc_final: 0.7703 (t) REVERT: A 86 SER cc_start: 0.8987 (m) cc_final: 0.8661 (t) REVERT: A 108 ASN cc_start: 0.8699 (t0) cc_final: 0.8482 (t0) REVERT: E 41 TYR cc_start: 0.8336 (m-80) cc_final: 0.8041 (m-80) REVERT: F 25 ASN cc_start: 0.8048 (m110) cc_final: 0.7837 (m-40) REVERT: F 63 GLU cc_start: 0.8365 (tt0) cc_final: 0.8164 (tt0) REVERT: F 88 TYR cc_start: 0.8457 (m-10) cc_final: 0.8191 (m-10) REVERT: C 68 ASN cc_start: 0.8667 (t0) cc_final: 0.8418 (t0) REVERT: G 68 ASN cc_start: 0.8479 (m-40) cc_final: 0.7213 (m-40) REVERT: G 74 LYS cc_start: 0.8702 (mttm) cc_final: 0.8368 (mtmm) REVERT: D 79 ARG cc_start: 0.8552 (ttp-110) cc_final: 0.8155 (mtm-85) REVERT: D 105 GLU cc_start: 0.7944 (tp30) cc_final: 0.7667 (tm-30) REVERT: D 109 HIS cc_start: 0.8099 (m90) cc_final: 0.7611 (m-70) REVERT: H 59 MET cc_start: 0.9006 (tpp) cc_final: 0.8615 (tpp) REVERT: H 85 LYS cc_start: 0.8632 (mtmt) cc_final: 0.8415 (mmtt) REVERT: L 6 LYS cc_start: 0.8458 (tttt) cc_final: 0.7744 (mmtt) REVERT: L 8 LEU cc_start: 0.4657 (mm) cc_final: 0.4070 (tt) REVERT: L 29 LYS cc_start: 0.8544 (mttt) cc_final: 0.8216 (tptp) REVERT: L 39 ASP cc_start: 0.7768 (p0) cc_final: 0.7449 (m-30) REVERT: L 71 LEU cc_start: 0.6967 (mt) cc_final: 0.6581 (mt) REVERT: K 27 TYR cc_start: 0.4974 (m-80) cc_final: 0.3655 (t80) REVERT: K 49 PRO cc_start: 0.6899 (Cg_exo) cc_final: 0.6655 (Cg_endo) outliers start: 8 outliers final: 1 residues processed: 389 average time/residue: 0.1790 time to fit residues: 92.1235 Evaluate side-chains 183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 182 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 98 optimal weight: 0.7980 chunk 107 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 9.9990 chunk 124 optimal weight: 20.0000 chunk 103 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 30.0000 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 25 ASN C 24 GLN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN D 49 HIS D 84 ASN D 95 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS K 252 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.104335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.074033 restraints weight = 44751.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073332 restraints weight = 33303.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.073438 restraints weight = 27193.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3172 r_free = 0.3172 target = 0.073724 restraints weight = 24918.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.073845 restraints weight = 22278.433| |-----------------------------------------------------------------------------| r_work (final): 0.3136 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15798 Z= 0.184 Angle : 0.748 7.355 22601 Z= 0.438 Chirality : 0.051 0.345 2569 Planarity : 0.005 0.061 1855 Dihedral : 29.732 161.284 4429 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.89 % Allowed : 14.50 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.20 (0.25), residues: 1098 helix: 0.69 (0.19), residues: 657 sheet: 0.51 (0.60), residues: 79 loop : -0.85 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG K 42 TYR 0.027 0.002 TYR H 83 PHE 0.037 0.002 PHE L 4 TRP 0.022 0.003 TRP K 228 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (15798) covalent geometry : angle 0.74842 / 0.44 (22601) hydrogen bonds : bond 0.06742 / 4.31 ( 830) hydrogen bonds : angle 3.78067 / 2.66 ( 2107) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 220 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8452 (m-80) cc_final: 0.8119 (m-80) REVERT: F 82 THR cc_start: 0.8938 (p) cc_final: 0.8365 (p) REVERT: F 85 ASP cc_start: 0.7239 (m-30) cc_final: 0.7034 (m-30) REVERT: C 61 GLU cc_start: 0.7999 (tt0) cc_final: 0.7720 (tt0) REVERT: G 16 THR cc_start: 0.9344 (OUTLIER) cc_final: 0.8995 (p) REVERT: G 64 GLU cc_start: 0.7264 (tm-30) cc_final: 0.6882 (tm-30) REVERT: D 59 MET cc_start: 0.9063 (tpp) cc_final: 0.8726 (tpp) REVERT: H 34 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8593 (mmtm) REVERT: H 59 MET cc_start: 0.8857 (tpp) cc_final: 0.8497 (tpp) REVERT: H 105 GLU cc_start: 0.7527 (pm20) cc_final: 0.7216 (pm20) REVERT: H 108 LYS cc_start: 0.8876 (mtmm) cc_final: 0.8195 (mtmm) REVERT: L 6 LYS cc_start: 0.8273 (tttt) cc_final: 0.7730 (mmtt) REVERT: L 8 LEU cc_start: 0.4638 (mm) cc_final: 0.4193 (tt) REVERT: K 10 LYS cc_start: 0.5003 (tppt) cc_final: 0.4110 (ttmm) REVERT: K 31 HIS cc_start: 0.4874 (OUTLIER) cc_final: 0.4427 (m90) REVERT: K 49 PRO cc_start: 0.6763 (Cg_exo) cc_final: 0.6520 (Cg_endo) outliers start: 37 outliers final: 14 residues processed: 243 average time/residue: 0.1237 time to fit residues: 43.9925 Evaluate side-chains 184 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 168 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 44 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 1.9990 chunk 104 optimal weight: 0.0980 chunk 111 optimal weight: 20.0000 chunk 109 optimal weight: 30.0000 chunk 89 optimal weight: 0.0970 chunk 23 optimal weight: 1.9990 chunk 135 optimal weight: 30.0000 chunk 11 optimal weight: 0.8980 chunk 108 optimal weight: 30.0000 chunk 116 optimal weight: 20.0000 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN F 25 ASN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN D 47 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.103442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.071596 restraints weight = 45086.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.072448 restraints weight = 32614.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.072446 restraints weight = 25245.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.072758 restraints weight = 22032.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.072723 restraints weight = 20337.033| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.3245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15798 Z= 0.161 Angle : 0.665 7.958 22601 Z= 0.392 Chirality : 0.047 0.335 2569 Planarity : 0.004 0.053 1855 Dihedral : 29.665 157.162 4428 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.10 % Allowed : 17.33 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 0.95 (0.26), residues: 1098 helix: 1.28 (0.20), residues: 656 sheet: 0.66 (0.60), residues: 79 loop : -0.48 (0.33), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 72 TYR 0.023 0.002 TYR H 83 PHE 0.019 0.001 PHE K 245 TRP 0.027 0.002 TRP K 228 HIS 0.008 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.16 (15798) covalent geometry : angle 0.66542 / 0.39 (22601) hydrogen bonds : bond 0.05811 / 3.77 ( 830) hydrogen bonds : angle 3.51382 / 2.48 ( 2107) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 183 time to evaluate : 0.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 41 TYR cc_start: 0.8494 (m-80) cc_final: 0.8268 (m-80) REVERT: B 74 GLU cc_start: 0.7595 (tp30) cc_final: 0.7310 (tp30) REVERT: B 84 MET cc_start: 0.8367 (tpp) cc_final: 0.8147 (tpp) REVERT: F 82 THR cc_start: 0.8947 (p) cc_final: 0.8461 (p) REVERT: F 85 ASP cc_start: 0.7405 (OUTLIER) cc_final: 0.7164 (m-30) REVERT: C 61 GLU cc_start: 0.8050 (tt0) cc_final: 0.7829 (tt0) REVERT: C 100 VAL cc_start: 0.9271 (t) cc_final: 0.9038 (p) REVERT: D 76 GLU cc_start: 0.8984 (mm-30) cc_final: 0.8766 (tp30) REVERT: D 105 GLU cc_start: 0.7142 (tm-30) cc_final: 0.6841 (tm-30) REVERT: D 109 HIS cc_start: 0.7732 (m90) cc_final: 0.7515 (m-70) REVERT: H 34 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8670 (mmtm) REVERT: H 59 MET cc_start: 0.8835 (tpp) cc_final: 0.8624 (tpp) REVERT: H 91 SER cc_start: 0.8421 (t) cc_final: 0.8144 (p) REVERT: L 8 LEU cc_start: 0.4721 (mm) cc_final: 0.4285 (tt) REVERT: L 39 ASP cc_start: 0.8278 (m-30) cc_final: 0.8017 (t0) REVERT: L 68 HIS cc_start: 0.6603 (m-70) cc_final: 0.6402 (m-70) REVERT: L 69 LEU cc_start: 0.6049 (OUTLIER) cc_final: 0.5835 (tp) REVERT: K 31 HIS cc_start: 0.4733 (OUTLIER) cc_final: 0.4218 (m90) REVERT: K 113 GLN cc_start: 0.5481 (OUTLIER) cc_final: 0.4546 (pp30) REVERT: K 153 MET cc_start: 0.7964 (ttm) cc_final: 0.7595 (ttm) outliers start: 39 outliers final: 25 residues processed: 205 average time/residue: 0.1188 time to fit residues: 36.2862 Evaluate side-chains 183 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 154 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 85 GLN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 110 ASN Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 21 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 123 optimal weight: 40.0000 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 80 optimal weight: 10.0000 chunk 133 optimal weight: 20.0000 chunk 112 optimal weight: 20.0000 chunk 79 optimal weight: 40.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.100054 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.067513 restraints weight = 44158.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.068251 restraints weight = 35234.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.068129 restraints weight = 29611.587| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068391 restraints weight = 25570.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.068414 restraints weight = 23762.061| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 15798 Z= 0.210 Angle : 0.702 7.285 22601 Z= 0.399 Chirality : 0.047 0.331 2569 Planarity : 0.005 0.040 1855 Dihedral : 29.678 155.131 4428 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.73 % Allowed : 18.38 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.18 (0.26), residues: 1098 helix: 1.45 (0.20), residues: 655 sheet: 0.39 (0.56), residues: 79 loop : -0.25 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 54 TYR 0.029 0.002 TYR D 83 PHE 0.020 0.002 PHE K 223 TRP 0.043 0.003 TRP K 228 HIS 0.010 0.002 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.21 (15798) covalent geometry : angle 0.70195 / 0.40 (22601) hydrogen bonds : bond 0.05864 / 3.84 ( 830) hydrogen bonds : angle 3.47931 / 2.47 ( 2107) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 156 time to evaluate : 0.430 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8989 (mp) REVERT: E 120 MET cc_start: 0.7880 (mtp) cc_final: 0.7624 (mtp) REVERT: F 85 ASP cc_start: 0.7704 (OUTLIER) cc_final: 0.7469 (m-30) REVERT: C 56 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6838 (tm-30) REVERT: C 61 GLU cc_start: 0.8153 (tt0) cc_final: 0.7897 (tt0) REVERT: G 56 GLU cc_start: 0.8054 (tm-30) cc_final: 0.7755 (tm-30) REVERT: G 64 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7668 (tm-30) REVERT: D 76 GLU cc_start: 0.9080 (mm-30) cc_final: 0.8791 (tp30) REVERT: H 34 LYS cc_start: 0.8889 (ttmm) cc_final: 0.8677 (mmtm) REVERT: H 91 SER cc_start: 0.8882 (t) cc_final: 0.8630 (p) REVERT: L 6 LYS cc_start: 0.8283 (tttt) cc_final: 0.7689 (mmtt) REVERT: L 8 LEU cc_start: 0.4715 (mm) cc_final: 0.4135 (tt) REVERT: L 39 ASP cc_start: 0.8416 (m-30) cc_final: 0.8129 (t0) REVERT: K 31 HIS cc_start: 0.4486 (OUTLIER) cc_final: 0.3947 (m90) REVERT: K 149 ASP cc_start: 0.8189 (m-30) cc_final: 0.7839 (p0) outliers start: 45 outliers final: 28 residues processed: 180 average time/residue: 0.1165 time to fit residues: 31.7492 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 140 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 80 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 39 optimal weight: 0.4980 chunk 89 optimal weight: 0.3980 chunk 9 optimal weight: 10.0000 chunk 25 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 72 optimal weight: 4.9990 chunk 2 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 117 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.101507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.068980 restraints weight = 44006.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.069490 restraints weight = 32635.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.069716 restraints weight = 24014.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069811 restraints weight = 22919.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.069807 restraints weight = 21144.443| |-----------------------------------------------------------------------------| r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8422 moved from start: 0.4101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 15798 Z= 0.140 Angle : 0.617 7.166 22601 Z= 0.364 Chirality : 0.044 0.335 2569 Planarity : 0.004 0.039 1855 Dihedral : 29.487 153.237 4428 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.68 % Allowed : 18.91 % Favored : 77.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.50 (0.26), residues: 1098 helix: 1.75 (0.21), residues: 648 sheet: 0.38 (0.56), residues: 79 loop : -0.13 (0.35), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 54 TYR 0.034 0.002 TYR D 83 PHE 0.011 0.001 PHE K 326 TRP 0.021 0.002 TRP K 228 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (15798) covalent geometry : angle 0.61689 / 0.36 (22601) hydrogen bonds : bond 0.04994 / 3.22 ( 830) hydrogen bonds : angle 3.23542 / 2.30 ( 2107) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 150 time to evaluate : 0.461 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9204 (OUTLIER) cc_final: 0.8955 (mp) REVERT: E 41 TYR cc_start: 0.8468 (m-80) cc_final: 0.8234 (m-80) REVERT: E 108 ASN cc_start: 0.9464 (t0) cc_final: 0.9244 (t0) REVERT: C 56 GLU cc_start: 0.7142 (OUTLIER) cc_final: 0.6840 (tm-30) REVERT: C 61 GLU cc_start: 0.8145 (tt0) cc_final: 0.7899 (tt0) REVERT: C 84 GLN cc_start: 0.9041 (OUTLIER) cc_final: 0.8077 (tt0) REVERT: G 16 THR cc_start: 0.9307 (OUTLIER) cc_final: 0.9042 (p) REVERT: G 56 GLU cc_start: 0.8060 (tm-30) cc_final: 0.7642 (tm-30) REVERT: G 64 GLU cc_start: 0.7825 (tm-30) cc_final: 0.7488 (tm-30) REVERT: D 76 GLU cc_start: 0.8988 (mm-30) cc_final: 0.8753 (tp30) REVERT: H 101 LEU cc_start: 0.8922 (mp) cc_final: 0.8714 (mt) REVERT: H 116 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8390 (ttmm) REVERT: L 6 LYS cc_start: 0.8300 (tttt) cc_final: 0.7651 (mmtt) REVERT: L 39 ASP cc_start: 0.8384 (m-30) cc_final: 0.8110 (t0) REVERT: K 31 HIS cc_start: 0.4557 (OUTLIER) cc_final: 0.3954 (m90) REVERT: K 153 MET cc_start: 0.7757 (ttm) cc_final: 0.7488 (ttm) outliers start: 35 outliers final: 18 residues processed: 169 average time/residue: 0.1096 time to fit residues: 28.3145 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 144 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 86 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 122 optimal weight: 40.0000 chunk 71 optimal weight: 30.0000 chunk 13 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 40 optimal weight: 4.9990 chunk 55 optimal weight: 4.9990 chunk 115 optimal weight: 20.0000 chunk 51 optimal weight: 0.6980 chunk 32 optimal weight: 1.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 85 GLN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.097819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.064906 restraints weight = 43719.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.065467 restraints weight = 35398.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.065391 restraints weight = 28966.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065633 restraints weight = 25669.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.065665 restraints weight = 23579.833| |-----------------------------------------------------------------------------| r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.4516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15798 Z= 0.259 Angle : 0.750 10.314 22601 Z= 0.413 Chirality : 0.047 0.332 2569 Planarity : 0.005 0.044 1855 Dihedral : 29.651 153.362 4428 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.62 % Allowed : 19.22 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.16 (0.26), residues: 1098 helix: 1.46 (0.20), residues: 659 sheet: 0.29 (0.55), residues: 79 loop : -0.32 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 29 TYR 0.041 0.002 TYR D 83 PHE 0.014 0.002 PHE E 67 TRP 0.014 0.002 TRP K 205 HIS 0.008 0.002 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00566 / 0.26 (15798) covalent geometry : angle 0.75019 / 0.41 (22601) hydrogen bonds : bond 0.06075 / 4.00 ( 830) hydrogen bonds : angle 3.57970 / 2.54 ( 2107) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 146 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9065 (mp) REVERT: E 108 ASN cc_start: 0.9477 (t0) cc_final: 0.9219 (t0) REVERT: C 56 GLU cc_start: 0.7316 (OUTLIER) cc_final: 0.7038 (tm-30) REVERT: C 61 GLU cc_start: 0.8231 (tt0) cc_final: 0.7978 (tt0) REVERT: C 84 GLN cc_start: 0.9172 (OUTLIER) cc_final: 0.8239 (tt0) REVERT: G 24 GLN cc_start: 0.8298 (OUTLIER) cc_final: 0.8019 (mm110) REVERT: G 56 GLU cc_start: 0.8197 (tm-30) cc_final: 0.7916 (tm-30) REVERT: G 64 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7764 (tm-30) REVERT: D 76 GLU cc_start: 0.9097 (mm-30) cc_final: 0.8309 (tp30) REVERT: H 34 LYS cc_start: 0.8718 (mmtm) cc_final: 0.8446 (mmtm) REVERT: H 101 LEU cc_start: 0.9073 (mp) cc_final: 0.8869 (mt) REVERT: L 6 LYS cc_start: 0.8292 (tttt) cc_final: 0.7603 (mptt) REVERT: L 72 ARG cc_start: 0.6953 (ptt90) cc_final: 0.6617 (ptt90) REVERT: K 31 HIS cc_start: 0.4390 (OUTLIER) cc_final: 0.3746 (m90) REVERT: K 149 ASP cc_start: 0.8077 (m-30) cc_final: 0.7813 (p0) REVERT: K 153 MET cc_start: 0.7735 (ttm) cc_final: 0.7479 (ttm) outliers start: 44 outliers final: 28 residues processed: 178 average time/residue: 0.1081 time to fit residues: 29.6719 Evaluate side-chains 169 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 24 GLN Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 75 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 121 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 23 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 126 optimal weight: 20.0000 chunk 106 optimal weight: 8.9990 chunk 78 optimal weight: 2.9990 chunk 37 optimal weight: 0.9980 chunk 122 optimal weight: 30.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.098616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.065360 restraints weight = 43070.366| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.065662 restraints weight = 31911.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.065912 restraints weight = 23869.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.065983 restraints weight = 22693.863| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065964 restraints weight = 21057.655| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 moved from start: 0.4661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15798 Z= 0.188 Angle : 0.666 9.319 22601 Z= 0.379 Chirality : 0.045 0.333 2569 Planarity : 0.004 0.037 1855 Dihedral : 29.542 151.600 4428 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 10.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 3.47 % Allowed : 21.01 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.34 (0.26), residues: 1098 helix: 1.60 (0.20), residues: 659 sheet: 0.38 (0.56), residues: 79 loop : -0.25 (0.35), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 29 TYR 0.030 0.002 TYR D 83 PHE 0.016 0.001 PHE K 243 TRP 0.011 0.002 TRP K 205 HIS 0.007 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 (15798) covalent geometry : angle 0.66556 / 0.38 (22601) hydrogen bonds : bond 0.05380 / 3.51 ( 830) hydrogen bonds : angle 3.41462 / 2.42 ( 2107) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 142 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.9315 (OUTLIER) cc_final: 0.9023 (mp) REVERT: E 108 ASN cc_start: 0.9482 (t0) cc_final: 0.9232 (t0) REVERT: C 56 GLU cc_start: 0.7335 (OUTLIER) cc_final: 0.7057 (tm-30) REVERT: C 84 GLN cc_start: 0.9187 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: G 23 LEU cc_start: 0.8656 (mt) cc_final: 0.7928 (mt) REVERT: G 64 GLU cc_start: 0.8114 (tm-30) cc_final: 0.7720 (tm-30) REVERT: G 68 ASN cc_start: 0.8501 (m-40) cc_final: 0.7859 (t0) REVERT: D 35 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8367 (mm-30) REVERT: H 108 LYS cc_start: 0.8651 (mtmm) cc_final: 0.8031 (mtmm) REVERT: H 116 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8415 (ttmm) REVERT: L 6 LYS cc_start: 0.8298 (tttt) cc_final: 0.7576 (mptt) REVERT: L 72 ARG cc_start: 0.6949 (ptt90) cc_final: 0.6640 (ptt90) REVERT: K 31 HIS cc_start: 0.4523 (OUTLIER) cc_final: 0.3769 (m90) REVERT: K 153 MET cc_start: 0.7857 (ttm) cc_final: 0.7375 (ttm) REVERT: K 238 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8752 (mp) outliers start: 33 outliers final: 22 residues processed: 162 average time/residue: 0.1056 time to fit residues: 26.5810 Evaluate side-chains 163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 135 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 71 optimal weight: 8.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 0.0570 chunk 22 optimal weight: 0.9980 chunk 133 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 130 optimal weight: 20.0000 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 0.0370 chunk 29 optimal weight: 0.6980 overall best weight: 0.4976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN K 109 HIS ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.100412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.067529 restraints weight = 43811.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.068635 restraints weight = 33516.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.068596 restraints weight = 23664.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068750 restraints weight = 22469.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.068715 restraints weight = 20739.431| |-----------------------------------------------------------------------------| r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.062 15798 Z= 0.136 Angle : 0.621 13.578 22601 Z= 0.361 Chirality : 0.042 0.337 2569 Planarity : 0.004 0.043 1855 Dihedral : 29.382 150.710 4428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 2.73 % Allowed : 21.53 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.54 (0.26), residues: 1098 helix: 1.72 (0.20), residues: 656 sheet: 0.42 (0.58), residues: 79 loop : -0.04 (0.36), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 116 TYR 0.018 0.002 TYR H 83 PHE 0.011 0.001 PHE K 326 TRP 0.009 0.001 TRP K 228 HIS 0.007 0.001 HIS K 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.14 (15798) covalent geometry : angle 0.62100 / 0.36 (22601) hydrogen bonds : bond 0.04754 / 3.09 ( 830) hydrogen bonds : angle 3.26126 / 2.31 ( 2107) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 152 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9417 (t0) cc_final: 0.9115 (t0) REVERT: E 108 ASN cc_start: 0.9486 (t0) cc_final: 0.9242 (t0) REVERT: C 84 GLN cc_start: 0.9155 (OUTLIER) cc_final: 0.8241 (tt0) REVERT: G 64 GLU cc_start: 0.8143 (tm-30) cc_final: 0.7762 (tm-30) REVERT: G 68 ASN cc_start: 0.8460 (m-40) cc_final: 0.7834 (t0) REVERT: H 59 MET cc_start: 0.8906 (tpp) cc_final: 0.8599 (tpp) REVERT: H 116 LYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8437 (ttmm) REVERT: L 6 LYS cc_start: 0.8249 (tttt) cc_final: 0.7519 (mptt) REVERT: L 8 LEU cc_start: 0.4715 (mm) cc_final: 0.4003 (tt) REVERT: L 39 ASP cc_start: 0.7691 (t0) cc_final: 0.7428 (t0) REVERT: K 31 HIS cc_start: 0.4558 (OUTLIER) cc_final: 0.3730 (m90) REVERT: K 149 ASP cc_start: 0.7801 (m-30) cc_final: 0.7517 (p0) REVERT: K 153 MET cc_start: 0.7873 (ttm) cc_final: 0.7389 (ttm) REVERT: K 238 ILE cc_start: 0.8998 (OUTLIER) cc_final: 0.8727 (mp) outliers start: 26 outliers final: 16 residues processed: 168 average time/residue: 0.1094 time to fit residues: 28.3052 Evaluate side-chains 163 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 143 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 91 SER Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 10.0000 chunk 114 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 chunk 16 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 133 optimal weight: 20.0000 chunk 8 optimal weight: 0.5980 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.100101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.067350 restraints weight = 44118.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.068270 restraints weight = 34244.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.068276 restraints weight = 24471.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068445 restraints weight = 22667.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.068443 restraints weight = 21019.597| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.4892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 15798 Z= 0.144 Angle : 0.627 9.545 22601 Z= 0.361 Chirality : 0.042 0.332 2569 Planarity : 0.004 0.050 1855 Dihedral : 29.398 150.604 4428 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.10 % Allowed : 22.16 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.63 (0.26), residues: 1098 helix: 1.79 (0.20), residues: 655 sheet: 0.49 (0.59), residues: 79 loop : 0.02 (0.35), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG L 72 TYR 0.022 0.001 TYR B 88 PHE 0.021 0.001 PHE K 243 TRP 0.008 0.001 TRP K 205 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.14 (15798) covalent geometry : angle 0.62672 / 0.36 (22601) hydrogen bonds : bond 0.04782 / 3.14 ( 830) hydrogen bonds : angle 3.25874 / 2.31 ( 2107) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 0.384 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9442 (t0) cc_final: 0.9155 (t0) REVERT: E 108 ASN cc_start: 0.9478 (t0) cc_final: 0.9236 (t0) REVERT: C 84 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8191 (tt0) REVERT: G 64 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7807 (tm-30) REVERT: G 68 ASN cc_start: 0.8437 (m-40) cc_final: 0.7836 (t0) REVERT: H 59 MET cc_start: 0.8936 (tpp) cc_final: 0.8673 (tpp) REVERT: H 116 LYS cc_start: 0.8922 (OUTLIER) cc_final: 0.8444 (ttmm) REVERT: L 6 LYS cc_start: 0.8299 (tttt) cc_final: 0.7579 (mptt) REVERT: L 8 LEU cc_start: 0.4695 (mm) cc_final: 0.3970 (tt) REVERT: K 31 HIS cc_start: 0.4568 (OUTLIER) cc_final: 0.3738 (m90) REVERT: K 149 ASP cc_start: 0.7896 (m-30) cc_final: 0.7509 (p0) REVERT: K 153 MET cc_start: 0.7904 (ttm) cc_final: 0.7438 (ttm) REVERT: K 238 ILE cc_start: 0.9007 (OUTLIER) cc_final: 0.8739 (mp) outliers start: 20 outliers final: 16 residues processed: 161 average time/residue: 0.1108 time to fit residues: 27.4426 Evaluate side-chains 164 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 144 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 57 optimal weight: 1.9990 chunk 112 optimal weight: 20.0000 chunk 22 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 80 optimal weight: 9.9990 chunk 10 optimal weight: 4.9990 chunk 69 optimal weight: 0.0020 chunk 92 optimal weight: 0.7980 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... F 75 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.100792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.068128 restraints weight = 44219.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069083 restraints weight = 33775.360| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.069076 restraints weight = 24029.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069300 restraints weight = 21963.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.069276 restraints weight = 20949.652| |-----------------------------------------------------------------------------| r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.4996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15798 Z= 0.137 Angle : 0.626 14.859 22601 Z= 0.358 Chirality : 0.042 0.331 2569 Planarity : 0.004 0.036 1855 Dihedral : 29.352 149.520 4428 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 2.10 % Allowed : 23.32 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.65 (0.26), residues: 1098 helix: 1.81 (0.20), residues: 655 sheet: 0.48 (0.57), residues: 80 loop : 0.02 (0.35), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG L 72 TYR 0.020 0.001 TYR B 88 PHE 0.009 0.001 PHE K 243 TRP 0.008 0.001 TRP K 205 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.14 (15798) covalent geometry : angle 0.62566 / 0.36 (22601) hydrogen bonds : bond 0.04613 / 3.02 ( 830) hydrogen bonds : angle 3.29232 / 2.33 ( 2107) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2196 Ramachandran restraints generated. 1098 Oldfield, 0 Emsley, 1098 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 154 time to evaluate : 0.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.9445 (t0) cc_final: 0.9146 (t0) REVERT: E 108 ASN cc_start: 0.9461 (t0) cc_final: 0.9227 (t0) REVERT: C 84 GLN cc_start: 0.9146 (OUTLIER) cc_final: 0.8209 (tt0) REVERT: G 64 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7756 (tm-30) REVERT: G 68 ASN cc_start: 0.8436 (m-40) cc_final: 0.7841 (t0) REVERT: H 35 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7540 (pp20) REVERT: H 59 MET cc_start: 0.8932 (tpp) cc_final: 0.8653 (tpp) REVERT: H 116 LYS cc_start: 0.8968 (OUTLIER) cc_final: 0.8476 (ttmm) REVERT: L 6 LYS cc_start: 0.8426 (tttt) cc_final: 0.7679 (mptt) REVERT: L 8 LEU cc_start: 0.4649 (mm) cc_final: 0.3941 (tt) REVERT: L 69 LEU cc_start: 0.6404 (tp) cc_final: 0.6158 (tp) REVERT: K 31 HIS cc_start: 0.4488 (OUTLIER) cc_final: 0.3631 (m90) REVERT: K 149 ASP cc_start: 0.7876 (m-30) cc_final: 0.7529 (p0) REVERT: K 153 MET cc_start: 0.7926 (ttm) cc_final: 0.7407 (ttm) REVERT: K 238 ILE cc_start: 0.8981 (OUTLIER) cc_final: 0.8729 (mp) REVERT: K 291 MET cc_start: 0.7402 (tpp) cc_final: 0.7142 (tpt) outliers start: 20 outliers final: 14 residues processed: 165 average time/residue: 0.1137 time to fit residues: 28.5138 Evaluate side-chains 167 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 149 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain B residue 53 GLU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 43 LEU Chi-restraints excluded: chain L residue 44 ILE Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 31 HIS Chi-restraints excluded: chain K residue 55 MET Chi-restraints excluded: chain K residue 238 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 130 optimal weight: 20.0000 chunk 103 optimal weight: 0.9980 chunk 114 optimal weight: 20.0000 chunk 5 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 134 optimal weight: 20.0000 chunk 133 optimal weight: 20.0000 chunk 37 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 0.0270 overall best weight: 1.1240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.100303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2980 r_free = 0.2980 target = 0.064496 restraints weight = 43545.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.065837 restraints weight = 26903.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.066716 restraints weight = 20174.621| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067122 restraints weight = 17196.776| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.067444 restraints weight = 15928.937| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.5102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15798 Z= 0.142 Angle : 0.622 11.157 22601 Z= 0.356 Chirality : 0.042 0.329 2569 Planarity : 0.004 0.036 1855 Dihedral : 29.378 149.070 4428 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.00 % Allowed : 23.53 % Favored : 74.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % 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: 1.72 (0.26), residues: 1098 helix: 1.87 (0.20), residues: 657 sheet: 0.44 (0.57), residues: 80 loop : 0.04 (0.36), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 116 TYR 0.021 0.001 TYR B 88 PHE 0.011 0.001 PHE K 243 TRP 0.009 0.001 TRP K 205 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.14 (15798) covalent geometry : angle 0.62181 / 0.36 (22601) hydrogen bonds : bond 0.04684 / 3.08 ( 830) hydrogen bonds : angle 3.29764 / 2.31 ( 2107) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2130.93 seconds wall clock time: 37 minutes 34.33 seconds (2254.33 seconds total)