Starting phenix.real_space_refine on Tue Nov 19 12:38:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_0468.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_0468.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_0468.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_0468.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nog_0468/11_2024/6nog_0468.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: {'TYR:plan': 2, 'ASN:plan1': 1, '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: 8.33, per 1000 atoms: 0.56 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: 3.58 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 6.20 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: 5.83 Time building geometry restraints manager: 4.20 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=" N PRO G 80 " pdb=" CD PRO G 80 " ideal model delta sigma weight residual 1.473 1.422 0.051 1.40e-02 5.10e+03 1.35e+01 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.495 -0.073 3.00e-02 1.11e+03 5.90e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.494 -0.072 3.00e-02 1.11e+03 5.75e+00 bond pdb=" C HIS H 49 " pdb=" N PRO H 50 " ideal model delta sigma weight residual 1.336 1.308 0.028 1.20e-02 6.94e+03 5.60e+00 bond pdb=" C GLY G 46 " pdb=" N ALA G 47 " ideal model delta sigma weight residual 1.332 1.300 0.032 1.38e-02 5.25e+03 5.22e+00 ... (remaining 15793 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.48: 21640 2.48 - 4.97: 856 4.97 - 7.45: 80 7.45 - 9.93: 21 9.93 - 12.41: 4 Bond angle restraints: 22601 Sorted by residual: 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 angle pdb=" N GLY G 105 " pdb=" CA GLY G 105 " pdb=" C GLY G 105 " ideal model delta sigma weight residual 113.18 124.85 -11.67 2.37e+00 1.78e-01 2.43e+01 angle pdb=" C ASP G 90 " pdb=" N GLU G 91 " pdb=" CA GLU G 91 " ideal model delta sigma weight residual 120.54 127.15 -6.61 1.35e+00 5.49e-01 2.40e+01 angle pdb=" N GLY C 46 " pdb=" CA GLY C 46 " pdb=" C GLY C 46 " ideal model delta sigma weight residual 114.66 120.63 -5.97 1.24e+00 6.50e-01 2.32e+01 angle pdb=" N ASP F 24 " pdb=" CA ASP F 24 " pdb=" C ASP F 24 " ideal model delta sigma weight residual 111.30 117.58 -6.28 1.36e+00 5.41e-01 2.13e+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: 2041 0.071 - 0.142: 445 0.142 - 0.213: 63 0.213 - 0.284: 12 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: 0.840 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.480 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 37.580 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7952 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 : 0.009 0.073 15798 Z= 0.556 Angle : 1.118 12.415 22601 Z= 0.660 Chirality : 0.062 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (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 TRP 0.030 0.004 TRP K 208 HIS 0.008 0.003 HIS E 113 PHE 0.032 0.004 PHE K 159 TYR 0.030 0.004 TYR K 27 ARG 0.010 0.001 ARG K 203 *********************** 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 : 1.254 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: symmetry clash REVERT: A 60 LEU cc_start: 0.8253 (mt) cc_final: 0.7951 (mt) REVERT: A 80 THR cc_start: 0.8160 (t) cc_final: 0.7703 (t) REVERT: A 86 SER cc_start: 0.8987 (m) cc_final: 0.8662 (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: 0.7809 (m-40) REVERT: F 63 GLU cc_start: 0.8364 (tt0) cc_final: 0.8164 (tt0) REVERT: F 88 TYR cc_start: 0.8458 (m-10) cc_final: 0.8190 (m-10) REVERT: C 68 ASN cc_start: 0.8668 (t0) cc_final: 0.8417 (t0) REVERT: G 68 ASN cc_start: 0.8479 (m-40) cc_final: 0.7210 (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: 0.8153 (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: D 121 TYR cc_start: 0.8029 (t80) cc_final: 0.7672 (t80) 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: 0.4074 (tt) REVERT: L 29 LYS cc_start: 0.8544 (mttt) cc_final: 0.8217 (tptp) REVERT: L 39 ASP cc_start: 0.7768 (p0) cc_final: 0.7447 (m-30) REVERT: L 71 LEU cc_start: 0.6967 (mt) cc_final: 0.6582 (mt) REVERT: K 27 TYR cc_start: 0.4974 (m-80) cc_final: 0.3654 (t80) REVERT: K 49 PRO cc_start: 0.6899 (Cg_exo) cc_final: 0.6654 (Cg_endo) outliers start: 8 outliers final: 1 residues processed: 389 average time/residue: 0.4055 time to fit residues: 205.2478 Evaluate side-chains 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 184 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 114 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 57 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 64 optimal weight: 4.9990 chunk 79 optimal weight: 2.9990 chunk 123 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN C 38 ASN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN D 49 HIS D 95 GLN ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 251 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 15798 Z= 0.328 Angle : 0.703 6.804 22601 Z= 0.404 Chirality : 0.040 0.190 2569 Planarity : 0.006 0.053 1855 Dihedral : 29.323 157.294 4429 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 4.62 % Allowed : 15.44 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.25), residues: 1098 helix: 0.75 (0.20), residues: 660 sheet: 0.62 (0.59), residues: 79 loop : -0.82 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP K 228 HIS 0.011 0.002 HIS K 117 PHE 0.033 0.003 PHE L 4 TYR 0.020 0.002 TYR F 88 ARG 0.008 0.001 ARG F 78 *********************** 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 235 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 191 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 GLU cc_start: 0.8046 (tp30) cc_final: 0.7796 (tp30) REVERT: B 84 MET cc_start: 0.8377 (tpp) cc_final: 0.8143 (tpp) REVERT: F 25 ASN cc_start: 0.8365 (m110) cc_final: 0.8027 (m-40) REVERT: F 63 GLU cc_start: 0.8366 (tt0) cc_final: 0.8122 (tt0) REVERT: F 88 TYR cc_start: 0.8388 (m-10) cc_final: 0.8165 (m-10) REVERT: C 61 GLU cc_start: 0.8467 (tt0) cc_final: 0.8141 (tt0) REVERT: G 16 THR cc_start: 0.9337 (OUTLIER) cc_final: 0.9096 (p) REVERT: G 56 GLU cc_start: 0.8270 (tm-30) cc_final: 0.8059 (tm-30) REVERT: G 64 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7614 (tm-30) REVERT: G 68 ASN cc_start: 0.8292 (m-40) cc_final: 0.7856 (m-40) REVERT: G 74 LYS cc_start: 0.8897 (mttm) cc_final: 0.8585 (mtmm) REVERT: D 82 HIS cc_start: 0.8372 (m-70) cc_final: 0.8166 (m170) REVERT: H 34 LYS cc_start: 0.8870 (ttmm) cc_final: 0.8530 (mmtm) REVERT: H 85 LYS cc_start: 0.8776 (mtmt) cc_final: 0.8508 (mmtt) REVERT: H 91 SER cc_start: 0.9175 (t) cc_final: 0.8777 (p) REVERT: L 6 LYS cc_start: 0.8406 (tttt) cc_final: 0.7669 (mmtt) REVERT: L 8 LEU cc_start: 0.4781 (mm) cc_final: 0.4312 (tt) REVERT: K 31 HIS cc_start: 0.4938 (OUTLIER) cc_final: 0.4169 (m90) REVERT: K 252 GLN cc_start: 0.8993 (mt0) cc_final: 0.8700 (mm-40) outliers start: 44 outliers final: 18 residues processed: 221 average time/residue: 0.2816 time to fit residues: 90.2189 Evaluate side-chains 172 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 93 GLN 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 B residue 62 LEU Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 74 GLU 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 D residue 51 ASP 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 36 ILE 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 68 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 84 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 123 optimal weight: 10.0000 chunk 133 optimal weight: 6.9990 chunk 110 optimal weight: 6.9990 chunk 122 optimal weight: 10.0000 chunk 42 optimal weight: 5.9990 chunk 99 optimal weight: 5.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 85 GLN G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 49 GLN K 31 HIS K 109 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 moved from start: 0.4400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15798 Z= 0.372 Angle : 0.683 6.745 22601 Z= 0.393 Chirality : 0.040 0.171 2569 Planarity : 0.005 0.051 1855 Dihedral : 29.184 154.995 4428 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer: Outliers : 4.73 % Allowed : 17.75 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.82 (0.26), residues: 1098 helix: 1.18 (0.20), residues: 662 sheet: 0.52 (0.57), residues: 80 loop : -0.55 (0.34), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP K 228 HIS 0.009 0.002 HIS K 117 PHE 0.016 0.002 PHE K 326 TYR 0.031 0.002 TYR F 88 ARG 0.005 0.001 ARG E 116 *********************** 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 202 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 157 time to evaluate : 1.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8211 (mtm180) cc_final: 0.7783 (mtm-85) REVERT: A 87 SER cc_start: 0.9302 (m) cc_final: 0.8922 (t) REVERT: E 90 MET cc_start: 0.9118 (mmm) cc_final: 0.8761 (mmp) REVERT: E 105 GLU cc_start: 0.8028 (tp30) cc_final: 0.7700 (tp30) REVERT: B 74 GLU cc_start: 0.8196 (tp30) cc_final: 0.7964 (tp30) REVERT: B 84 MET cc_start: 0.8287 (tpp) cc_final: 0.7872 (tpp) REVERT: F 63 GLU cc_start: 0.8327 (tt0) cc_final: 0.8058 (tt0) REVERT: C 61 GLU cc_start: 0.8461 (tt0) cc_final: 0.8066 (tt0) REVERT: C 84 GLN cc_start: 0.9016 (OUTLIER) cc_final: 0.8024 (tt0) REVERT: G 64 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7880 (tm-30) REVERT: G 68 ASN cc_start: 0.8436 (m-40) cc_final: 0.7671 (t0) REVERT: G 74 LYS cc_start: 0.8998 (mttm) cc_final: 0.8700 (mtmm) REVERT: D 35 GLU cc_start: 0.8614 (mm-30) cc_final: 0.8235 (mm-30) REVERT: D 76 GLU cc_start: 0.9211 (tp30) cc_final: 0.8878 (tp30) REVERT: D 82 HIS cc_start: 0.8285 (m-70) cc_final: 0.8048 (m170) REVERT: H 34 LYS cc_start: 0.8825 (ttmm) cc_final: 0.8588 (mmtm) REVERT: H 35 GLU cc_start: 0.8365 (pp20) cc_final: 0.7981 (pp20) REVERT: H 59 MET cc_start: 0.8913 (tpp) cc_final: 0.8571 (tpp) REVERT: H 85 LYS cc_start: 0.8860 (mtmt) cc_final: 0.8551 (mmtt) REVERT: H 116 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8571 (ttmm) REVERT: L 6 LYS cc_start: 0.8481 (tttt) cc_final: 0.7641 (mptt) REVERT: L 8 LEU cc_start: 0.4748 (mm) cc_final: 0.4175 (tt) REVERT: L 29 LYS cc_start: 0.8439 (mttt) cc_final: 0.8152 (tptt) REVERT: L 33 LYS cc_start: 0.6458 (OUTLIER) cc_final: 0.6183 (ptmt) REVERT: L 39 ASP cc_start: 0.8168 (t0) cc_final: 0.7934 (t0) REVERT: K 31 HIS cc_start: 0.4686 (OUTLIER) cc_final: 0.4155 (m90) REVERT: K 216 TYR cc_start: 0.4202 (p90) cc_final: 0.3740 (p90) REVERT: K 252 GLN cc_start: 0.8965 (mt0) cc_final: 0.8689 (mm-40) outliers start: 45 outliers final: 33 residues processed: 187 average time/residue: 0.2700 time to fit residues: 74.2962 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 142 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 96 SER 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 B residue 46 ILE Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 ASN 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 G residue 107 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 33 LYS Chi-restraints excluded: chain L residue 36 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 151 ILE Chi-restraints excluded: chain K residue 217 THR 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 122 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 83 optimal weight: 8.9990 chunk 124 optimal weight: 7.9990 chunk 131 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 35 optimal weight: 2.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN K 31 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.4870 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15798 Z= 0.349 Angle : 0.653 7.065 22601 Z= 0.377 Chirality : 0.039 0.154 2569 Planarity : 0.005 0.040 1855 Dihedral : 29.111 154.033 4428 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 5.46 % Allowed : 18.38 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.26), residues: 1098 helix: 1.32 (0.20), residues: 663 sheet: 0.38 (0.56), residues: 80 loop : -0.41 (0.35), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP K 228 HIS 0.020 0.002 HIS K 31 PHE 0.014 0.002 PHE K 326 TYR 0.019 0.002 TYR H 83 ARG 0.012 0.001 ARG L 72 *********************** 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 200 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 148 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8222 (mtm180) cc_final: 0.7855 (mtm-85) REVERT: A 87 SER cc_start: 0.9226 (m) cc_final: 0.8830 (t) REVERT: E 105 GLU cc_start: 0.8051 (tp30) cc_final: 0.7714 (tp30) REVERT: E 108 ASN cc_start: 0.9207 (t0) cc_final: 0.9003 (t0) REVERT: E 133 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7879 (mt-10) REVERT: B 74 GLU cc_start: 0.8237 (tp30) cc_final: 0.7952 (tp30) REVERT: B 84 MET cc_start: 0.8353 (tpp) cc_final: 0.8104 (tpp) REVERT: F 63 GLU cc_start: 0.8309 (tt0) cc_final: 0.8070 (tt0) REVERT: C 61 GLU cc_start: 0.8482 (tt0) cc_final: 0.8168 (tt0) REVERT: C 84 GLN cc_start: 0.9053 (OUTLIER) cc_final: 0.8105 (tt0) REVERT: G 68 ASN cc_start: 0.8522 (m-40) cc_final: 0.7824 (t0) REVERT: G 74 LYS cc_start: 0.8988 (mttm) cc_final: 0.8694 (mtmm) REVERT: D 35 GLU cc_start: 0.8622 (mm-30) cc_final: 0.8113 (mm-30) REVERT: D 76 GLU cc_start: 0.9193 (tp30) cc_final: 0.8758 (tp30) REVERT: H 34 LYS cc_start: 0.8909 (ttmm) cc_final: 0.8650 (mmtm) REVERT: H 85 LYS cc_start: 0.8868 (mtmt) cc_final: 0.8520 (mmtt) REVERT: H 116 LYS cc_start: 0.9063 (OUTLIER) cc_final: 0.8588 (ttmm) REVERT: L 6 LYS cc_start: 0.8514 (tttt) cc_final: 0.7613 (mptt) REVERT: L 29 LYS cc_start: 0.8467 (mttt) cc_final: 0.8112 (tptt) REVERT: L 39 ASP cc_start: 0.8272 (t0) cc_final: 0.8010 (t0) REVERT: K 149 ASP cc_start: 0.8045 (m-30) cc_final: 0.7624 (p0) REVERT: K 238 ILE cc_start: 0.9222 (OUTLIER) cc_final: 0.8871 (mp) REVERT: K 252 GLN cc_start: 0.8982 (mt0) cc_final: 0.8767 (mt0) outliers start: 52 outliers final: 33 residues processed: 184 average time/residue: 0.2686 time to fit residues: 73.2463 Evaluate side-chains 176 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 139 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 74 GLU Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 91 SER 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 116 LYS Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 36 ILE Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 217 THR Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 74 optimal weight: 9.9990 chunk 1 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 54 optimal weight: 0.8980 chunk 112 optimal weight: 6.9990 chunk 90 optimal weight: 7.9990 chunk 0 optimal weight: 7.9990 chunk 67 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 33 optimal weight: 0.0270 chunk 44 optimal weight: 5.9990 overall best weight: 3.1844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.5341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 15798 Z= 0.365 Angle : 0.659 8.752 22601 Z= 0.378 Chirality : 0.039 0.157 2569 Planarity : 0.005 0.044 1855 Dihedral : 29.183 151.645 4428 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 5.36 % Allowed : 18.91 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.26), residues: 1098 helix: 1.29 (0.20), residues: 666 sheet: 0.56 (0.57), residues: 80 loop : -0.43 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP K 228 HIS 0.005 0.001 HIS C 31 PHE 0.012 0.002 PHE K 326 TYR 0.026 0.002 TYR D 83 ARG 0.009 0.001 ARG L 72 *********************** 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 199 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 148 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 83 ARG cc_start: 0.8207 (mtm180) cc_final: 0.7830 (mtm-85) REVERT: A 87 SER cc_start: 0.9205 (m) cc_final: 0.8815 (t) REVERT: E 73 GLU cc_start: 0.8752 (tt0) cc_final: 0.8050 (tt0) REVERT: E 105 GLU cc_start: 0.8107 (tp30) cc_final: 0.7865 (tp30) REVERT: E 108 ASN cc_start: 0.9227 (t0) cc_final: 0.9009 (t0) REVERT: E 133 GLU cc_start: 0.8122 (OUTLIER) cc_final: 0.7890 (mt-10) REVERT: B 74 GLU cc_start: 0.8234 (tp30) cc_final: 0.8032 (tp30) REVERT: F 25 ASN cc_start: 0.8755 (m110) cc_final: 0.8239 (m110) REVERT: F 63 GLU cc_start: 0.8309 (tt0) cc_final: 0.8103 (tt0) REVERT: C 56 GLU cc_start: 0.8123 (tm-30) cc_final: 0.7834 (tm-30) REVERT: C 61 GLU cc_start: 0.8464 (tt0) cc_final: 0.8136 (tt0) REVERT: C 84 GLN cc_start: 0.9121 (OUTLIER) cc_final: 0.8154 (tt0) REVERT: G 74 LYS cc_start: 0.8994 (mttm) cc_final: 0.8720 (mtmm) REVERT: D 35 GLU cc_start: 0.8589 (mm-30) cc_final: 0.8061 (mm-30) REVERT: D 76 GLU cc_start: 0.9208 (tp30) cc_final: 0.8785 (tp30) REVERT: H 34 LYS cc_start: 0.8899 (ttmm) cc_final: 0.8663 (mmtm) REVERT: H 85 LYS cc_start: 0.8899 (mtmt) cc_final: 0.8472 (mmtt) REVERT: H 108 LYS cc_start: 0.8955 (mtmm) cc_final: 0.8527 (mtmt) REVERT: H 116 LYS cc_start: 0.9074 (OUTLIER) cc_final: 0.8595 (ttmm) REVERT: L 6 LYS cc_start: 0.8484 (tttt) cc_final: 0.7543 (mptt) REVERT: L 29 LYS cc_start: 0.8420 (mttt) cc_final: 0.8104 (tptt) REVERT: K 238 ILE cc_start: 0.9229 (OUTLIER) cc_final: 0.8899 (mp) REVERT: K 252 GLN cc_start: 0.8988 (mt0) cc_final: 0.8777 (mt0) outliers start: 51 outliers final: 30 residues processed: 190 average time/residue: 0.2819 time to fit residues: 78.3032 Evaluate side-chains 173 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 139 time to evaluate : 1.288 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU 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 27 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 118 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 77 optimal weight: 30.0000 chunk 32 optimal weight: 1.9990 chunk 131 optimal weight: 6.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 69 optimal weight: 0.9990 chunk 126 optimal weight: 6.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN F 75 HIS 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.5557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15798 Z= 0.293 Angle : 0.618 7.546 22601 Z= 0.359 Chirality : 0.037 0.176 2569 Planarity : 0.004 0.042 1855 Dihedral : 29.100 149.765 4428 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.62 % Allowed : 21.11 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.26), residues: 1098 helix: 1.45 (0.20), residues: 664 sheet: 0.60 (0.57), residues: 80 loop : -0.38 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP K 228 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.001 PHE K 326 TYR 0.024 0.002 TYR D 83 ARG 0.006 0.000 ARG L 72 *********************** 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 194 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 1.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9131 (m) cc_final: 0.8715 (t) REVERT: A 90 MET cc_start: 0.8740 (mmm) cc_final: 0.8353 (mmt) REVERT: E 90 MET cc_start: 0.8988 (mmm) cc_final: 0.8629 (mmp) REVERT: E 105 GLU cc_start: 0.8150 (tp30) cc_final: 0.7900 (tp30) REVERT: B 74 GLU cc_start: 0.8200 (tp30) cc_final: 0.7985 (tp30) REVERT: F 23 ARG cc_start: 0.7286 (ptm-80) cc_final: 0.6894 (ttm-80) REVERT: C 56 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7842 (tm-30) REVERT: C 61 GLU cc_start: 0.8463 (tt0) cc_final: 0.8112 (tt0) REVERT: C 84 GLN cc_start: 0.9124 (OUTLIER) cc_final: 0.8179 (tt0) REVERT: G 74 LYS cc_start: 0.8997 (mttm) cc_final: 0.8750 (mtmm) REVERT: D 35 GLU cc_start: 0.8586 (mm-30) cc_final: 0.8143 (mm-30) REVERT: D 76 GLU cc_start: 0.9213 (tp30) cc_final: 0.8788 (tp30) REVERT: H 34 LYS cc_start: 0.8826 (ttmm) cc_final: 0.8616 (mmtm) REVERT: H 40 TYR cc_start: 0.8986 (m-80) cc_final: 0.8785 (m-80) REVERT: H 59 MET cc_start: 0.9083 (tpp) cc_final: 0.8807 (tpp) REVERT: H 85 LYS cc_start: 0.8759 (mtmt) cc_final: 0.8379 (mmtt) REVERT: H 116 LYS cc_start: 0.9087 (OUTLIER) cc_final: 0.8569 (ttmm) REVERT: L 6 LYS cc_start: 0.8497 (tttt) cc_final: 0.7572 (mptt) REVERT: L 29 LYS cc_start: 0.8333 (mttt) cc_final: 0.7990 (tptt) REVERT: K 238 ILE cc_start: 0.9220 (OUTLIER) cc_final: 0.8897 (mp) REVERT: K 243 PHE cc_start: 0.7728 (OUTLIER) cc_final: 0.7506 (m-10) REVERT: K 252 GLN cc_start: 0.8992 (mt0) cc_final: 0.8791 (mt0) outliers start: 44 outliers final: 30 residues processed: 181 average time/residue: 0.2819 time to fit residues: 77.9070 Evaluate side-chains 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 141 time to evaluate : 1.441 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain C residue 27 VAL 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 G residue 113 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 151 ILE Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 96 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 73 optimal weight: 0.9990 chunk 131 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 52 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.5742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 15798 Z= 0.296 Angle : 0.626 10.120 22601 Z= 0.360 Chirality : 0.037 0.163 2569 Planarity : 0.004 0.043 1855 Dihedral : 29.112 149.103 4428 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 4.52 % Allowed : 21.74 % Favored : 73.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1098 helix: 1.46 (0.20), residues: 661 sheet: 0.62 (0.56), residues: 80 loop : -0.41 (0.35), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 228 HIS 0.005 0.001 HIS A 113 PHE 0.015 0.001 PHE K 326 TYR 0.028 0.002 TYR D 83 ARG 0.008 0.000 ARG A 116 *********************** 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 192 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 149 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9129 (m) cc_final: 0.8733 (t) REVERT: A 90 MET cc_start: 0.8814 (mmm) cc_final: 0.8393 (mmt) REVERT: E 90 MET cc_start: 0.8956 (mmm) cc_final: 0.8638 (mmp) REVERT: E 105 GLU cc_start: 0.8175 (tp30) cc_final: 0.7905 (tp30) REVERT: B 74 GLU cc_start: 0.8173 (tp30) cc_final: 0.7952 (tp30) REVERT: F 23 ARG cc_start: 0.7426 (ptm-80) cc_final: 0.6942 (ttm-80) REVERT: C 56 GLU cc_start: 0.8109 (tm-30) cc_final: 0.7865 (tm-30) REVERT: C 61 GLU cc_start: 0.8449 (tt0) cc_final: 0.8111 (tt0) REVERT: C 84 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8193 (tt0) REVERT: G 74 LYS cc_start: 0.8987 (mttm) cc_final: 0.8750 (mtmm) REVERT: D 35 GLU cc_start: 0.8525 (mm-30) cc_final: 0.8206 (mm-30) REVERT: D 76 GLU cc_start: 0.9217 (tp30) cc_final: 0.8804 (tp30) REVERT: H 85 LYS cc_start: 0.8769 (mtmt) cc_final: 0.8378 (mmtt) REVERT: H 116 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8561 (ttmm) REVERT: L 6 LYS cc_start: 0.8476 (tttt) cc_final: 0.7526 (mptt) REVERT: L 29 LYS cc_start: 0.8359 (mttt) cc_final: 0.7793 (tptp) REVERT: K 149 ASP cc_start: 0.7979 (m-30) cc_final: 0.7593 (p0) REVERT: K 238 ILE cc_start: 0.9141 (OUTLIER) cc_final: 0.8822 (mp) REVERT: K 243 PHE cc_start: 0.7741 (OUTLIER) cc_final: 0.7461 (m-10) REVERT: K 252 GLN cc_start: 0.9006 (mt0) cc_final: 0.8803 (mt0) outliers start: 43 outliers final: 36 residues processed: 181 average time/residue: 0.2828 time to fit residues: 78.0346 Evaluate side-chains 179 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 139 time to evaluate : 1.370 ------------------------------------------------------------------------------- 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 96 SER Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU 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 E residue 124 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU 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 27 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 84 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 109 HIS Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 0.5980 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 83 optimal weight: 9.9990 chunk 89 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 103 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 125 optimal weight: 6.9990 chunk 114 optimal weight: 7.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15798 Z= 0.239 Angle : 0.595 11.078 22601 Z= 0.344 Chirality : 0.036 0.154 2569 Planarity : 0.004 0.047 1855 Dihedral : 28.998 149.086 4428 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.47 % Allowed : 22.69 % Favored : 73.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.26), residues: 1098 helix: 1.60 (0.20), residues: 662 sheet: 0.63 (0.57), residues: 80 loop : -0.31 (0.35), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 228 HIS 0.005 0.001 HIS A 113 PHE 0.013 0.001 PHE K 326 TYR 0.015 0.001 TYR D 83 ARG 0.007 0.000 ARG A 116 *********************** 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 185 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 152 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9018 (m) cc_final: 0.8601 (t) REVERT: A 90 MET cc_start: 0.8718 (mmm) cc_final: 0.8338 (mmt) REVERT: A 108 ASN cc_start: 0.9283 (t0) cc_final: 0.8948 (t0) REVERT: E 90 MET cc_start: 0.8885 (mmm) cc_final: 0.8602 (mmp) REVERT: E 105 GLU cc_start: 0.8191 (tp30) cc_final: 0.7866 (tp30) REVERT: B 74 GLU cc_start: 0.8149 (tp30) cc_final: 0.7939 (tp30) REVERT: F 23 ARG cc_start: 0.7456 (ptm-80) cc_final: 0.6949 (ttm-80) REVERT: C 56 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7846 (tm-30) REVERT: C 84 GLN cc_start: 0.9133 (OUTLIER) cc_final: 0.8176 (tt0) REVERT: G 68 ASN cc_start: 0.8505 (m-40) cc_final: 0.7856 (t0) REVERT: G 74 LYS cc_start: 0.8991 (mttm) cc_final: 0.8747 (mtmm) REVERT: D 35 GLU cc_start: 0.8508 (mm-30) cc_final: 0.8238 (mm-30) REVERT: H 85 LYS cc_start: 0.8758 (mtmt) cc_final: 0.8363 (mmtt) REVERT: H 108 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8108 (mtmm) REVERT: H 116 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8551 (ttmm) REVERT: L 6 LYS cc_start: 0.8448 (tttt) cc_final: 0.7583 (mptt) REVERT: L 29 LYS cc_start: 0.8353 (mttt) cc_final: 0.7878 (tptt) REVERT: K 238 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8837 (mp) REVERT: K 243 PHE cc_start: 0.7581 (OUTLIER) cc_final: 0.7353 (m-10) outliers start: 33 outliers final: 23 residues processed: 175 average time/residue: 0.2649 time to fit residues: 69.3344 Evaluate side-chains 171 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 144 time to evaluate : 1.273 ------------------------------------------------------------------------------- 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 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 E residue 124 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 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 D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 122 optimal weight: 10.0000 chunk 125 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 95 optimal weight: 7.9990 chunk 37 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 115 optimal weight: 7.9990 chunk 121 optimal weight: 10.0000 chunk 80 optimal weight: 50.0000 chunk 129 optimal weight: 5.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.6104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.080 15798 Z= 0.530 Angle : 0.763 9.083 22601 Z= 0.426 Chirality : 0.044 0.172 2569 Planarity : 0.006 0.079 1855 Dihedral : 29.399 151.027 4428 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 4.62 % Allowed : 22.37 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.25), residues: 1098 helix: 1.10 (0.19), residues: 667 sheet: 0.47 (0.58), residues: 80 loop : -0.67 (0.34), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 22 HIS 0.007 0.002 HIS G 31 PHE 0.017 0.002 PHE K 159 TYR 0.020 0.003 TYR A 99 ARG 0.007 0.001 ARG A 116 *********************** 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 175 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 131 time to evaluate : 1.265 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9262 (m) cc_final: 0.8970 (t) REVERT: E 90 MET cc_start: 0.9011 (mmm) cc_final: 0.8788 (mmp) REVERT: E 105 GLU cc_start: 0.8146 (tp30) cc_final: 0.7885 (tp30) REVERT: B 74 GLU cc_start: 0.8299 (tp30) cc_final: 0.8094 (tp30) REVERT: F 23 ARG cc_start: 0.7518 (ptm-80) cc_final: 0.6984 (ttm-80) REVERT: C 56 GLU cc_start: 0.8242 (tm-30) cc_final: 0.7976 (tm-30) REVERT: C 84 GLN cc_start: 0.9145 (OUTLIER) cc_final: 0.8203 (tt0) REVERT: G 74 LYS cc_start: 0.9030 (mttm) cc_final: 0.8738 (mtmm) REVERT: D 35 GLU cc_start: 0.8470 (mm-30) cc_final: 0.7967 (mm-30) REVERT: H 85 LYS cc_start: 0.8862 (mtmt) cc_final: 0.8409 (mmtt) REVERT: L 6 LYS cc_start: 0.8461 (tttt) cc_final: 0.7648 (mptt) REVERT: L 29 LYS cc_start: 0.8227 (mttt) cc_final: 0.7568 (tptt) REVERT: L 30 ILE cc_start: 0.8269 (mm) cc_final: 0.7847 (mm) REVERT: L 33 LYS cc_start: 0.6378 (pptt) cc_final: 0.5484 (pttt) REVERT: K 96 MET cc_start: 0.2181 (mmm) cc_final: 0.1277 (mtp) REVERT: K 149 ASP cc_start: 0.8266 (m-30) cc_final: 0.7759 (p0) REVERT: K 238 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8768 (mp) REVERT: K 243 PHE cc_start: 0.7639 (OUTLIER) cc_final: 0.7358 (m-10) REVERT: K 252 GLN cc_start: 0.8973 (mt0) cc_final: 0.8571 (mm-40) outliers start: 44 outliers final: 35 residues processed: 168 average time/residue: 0.2624 time to fit residues: 66.1503 Evaluate side-chains 165 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 127 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 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 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 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 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 107 VAL Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 93 GLU Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 71 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 109 HIS Chi-restraints excluded: chain K residue 171 LEU Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 243 PHE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 78 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 89 optimal weight: 4.9990 chunk 135 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 107 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 66 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 114 optimal weight: 6.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 85 GLN ** E 108 ASN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15798 Z= 0.249 Angle : 0.621 9.814 22601 Z= 0.358 Chirality : 0.037 0.154 2569 Planarity : 0.004 0.049 1855 Dihedral : 29.095 150.400 4428 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.36 % Allowed : 23.84 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.16 (0.25), residues: 1098 helix: 1.50 (0.20), residues: 656 sheet: 0.49 (0.59), residues: 80 loop : -0.43 (0.34), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 228 HIS 0.005 0.001 HIS A 113 PHE 0.012 0.001 PHE K 326 TYR 0.022 0.002 TYR H 40 ARG 0.004 0.000 ARG L 72 ********************** 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 180 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 87 SER cc_start: 0.9029 (m) cc_final: 0.8624 (t) REVERT: A 90 MET cc_start: 0.8623 (mmm) cc_final: 0.8291 (mmt) REVERT: E 90 MET cc_start: 0.8929 (mmm) cc_final: 0.8689 (mmp) REVERT: E 105 GLU cc_start: 0.8175 (tp30) cc_final: 0.7915 (tp30) REVERT: B 74 GLU cc_start: 0.8169 (tp30) cc_final: 0.7950 (tp30) REVERT: F 23 ARG cc_start: 0.7484 (ptm-80) cc_final: 0.6961 (ttm-80) REVERT: F 84 MET cc_start: 0.7998 (tpp) cc_final: 0.7769 (tpp) REVERT: C 56 GLU cc_start: 0.8191 (tm-30) cc_final: 0.7945 (tm-30) REVERT: C 84 GLN cc_start: 0.9141 (OUTLIER) cc_final: 0.8178 (tt0) REVERT: G 68 ASN cc_start: 0.8517 (m-40) cc_final: 0.7985 (t0) REVERT: G 74 LYS cc_start: 0.8997 (mttm) cc_final: 0.8713 (mtmm) REVERT: D 35 GLU cc_start: 0.8426 (mm-30) cc_final: 0.8157 (mm-30) REVERT: H 85 LYS cc_start: 0.8775 (mtmt) cc_final: 0.8335 (mmtt) REVERT: H 116 LYS cc_start: 0.9085 (OUTLIER) cc_final: 0.8554 (ttmm) REVERT: L 6 LYS cc_start: 0.8493 (tttt) cc_final: 0.7674 (mptt) REVERT: L 29 LYS cc_start: 0.8264 (mttt) cc_final: 0.7588 (tptt) REVERT: L 33 LYS cc_start: 0.6511 (pptt) cc_final: 0.5729 (pttt) REVERT: K 96 MET cc_start: 0.2115 (mmm) cc_final: 0.1294 (mtp) REVERT: K 238 ILE cc_start: 0.9123 (OUTLIER) cc_final: 0.8775 (mp) REVERT: K 252 GLN cc_start: 0.8968 (mt0) cc_final: 0.8646 (mm-40) outliers start: 32 outliers final: 23 residues processed: 172 average time/residue: 0.2740 time to fit residues: 69.6071 Evaluate side-chains 168 residues out of total 960 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 1.279 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 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 90 LEU 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 84 GLN Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain H residue 116 LYS Chi-restraints excluded: chain L residue 69 LEU Chi-restraints excluded: chain L residue 73 LEU Chi-restraints excluded: chain K residue 109 HIS Chi-restraints excluded: chain K residue 238 ILE Chi-restraints excluded: chain K residue 317 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 136 random chunks: chunk 33 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 6 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS ** K 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 234 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.099094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.066547 restraints weight = 43140.345| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.065756 restraints weight = 29195.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.066229 restraints weight = 24570.872| |-----------------------------------------------------------------------------| r_work (final): 0.2977 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.6189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 15798 Z= 0.189 Angle : 0.586 10.192 22601 Z= 0.339 Chirality : 0.035 0.149 2569 Planarity : 0.004 0.050 1855 Dihedral : 28.829 148.810 4428 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.31 % Allowed : 24.89 % Favored : 72.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.63 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.26), residues: 1098 helix: 1.75 (0.20), residues: 654 sheet: 0.54 (0.59), residues: 80 loop : -0.29 (0.34), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 228 HIS 0.015 0.001 HIS H 82 PHE 0.010 0.001 PHE K 326 TYR 0.023 0.001 TYR H 40 ARG 0.004 0.000 ARG L 72 Origin is already at (0, 0, 0), no shifts will be applied Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_fail.pdb'. Return code: -15 Dumping stderr: