Starting phenix.real_space_refine on Mon Nov 18 06:41:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/11_2024/8evh_28629.cif" } resolution = 2.85 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= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 282 5.49 5 S 35 5.16 5 C 9256 2.51 5 N 2913 2.21 5 O 3591 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 16077 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 820 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 829 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 731 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 2889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2889 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain breaks: 1 Chain: "J" Number of atoms: 2892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 2892 Classifications: {'DNA': 141} Link IDs: {'rna3p': 140} Chain: "M" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "N" Number of atoms: 1769 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1769 Classifications: {'peptide': 226} Link IDs: {'PTRANS': 10, 'TRANS': 215} Chain breaks: 1 Chain: "O" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 746 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 9.00, per 1000 atoms: 0.56 Number of scatterers: 16077 At special positions: 0 Unit cell: (139.392, 128.832, 127.776, 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 35 16.00 P 282 15.00 O 3591 8.00 N 2913 7.00 C 9256 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS M 44 " - pdb=" SG CYS M 118 " distance=2.03 Simple disulfide: pdb=" SG CYS M 181 " - pdb=" SG CYS M 246 " distance=2.03 Simple disulfide: pdb=" SG CYS N 44 " - pdb=" SG CYS N 118 " distance=2.03 Simple disulfide: pdb=" SG CYS N 181 " - pdb=" SG CYS N 246 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.19 Conformation dependent library (CDL) restraints added in 1.4 seconds 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2420 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 47.6% alpha, 19.2% beta 137 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 7.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.036A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.747A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 92 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.514A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.742A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.519A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.780A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.421A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 120 removed outlier: 3.775A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'M' and resid 50 through 52 No H-bonds generated for 'chain 'M' and resid 50 through 52' Processing helix chain 'M' and resid 84 through 87 Processing helix chain 'M' and resid 109 through 113 removed outlier: 3.868A pdb=" N SER M 113 " --> pdb=" O SER M 110 " (cutoff:3.500A) Processing helix chain 'M' and resid 237 through 241 removed outlier: 3.539A pdb=" N THR M 241 " --> pdb=" O SER M 238 " (cutoff:3.500A) Processing helix chain 'N' and resid 50 through 52 No H-bonds generated for 'chain 'N' and resid 50 through 52' Processing helix chain 'N' and resid 109 through 113 removed outlier: 3.751A pdb=" N SER N 113 " --> pdb=" O SER N 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 237 through 241 removed outlier: 4.008A pdb=" N THR N 241 " --> pdb=" O SER N 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 172 through 185 removed outlier: 4.062A pdb=" N GLN O 176 " --> pdb=" O ILE O 172 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LEU O 182 " --> pdb=" O LEU O 178 " (cutoff:3.500A) Processing helix chain 'O' and resid 207 through 220 Processing helix chain 'O' and resid 226 through 241 removed outlier: 3.783A pdb=" N ALA O 233 " --> pdb=" O LYS O 229 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N LEU O 234 " --> pdb=" O MET O 230 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ASN O 236 " --> pdb=" O ARG O 232 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N TYR O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLY O 238 " --> pdb=" O LEU O 234 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N LYS O 239 " --> pdb=" O ARG O 235 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N THR O 240 " --> pdb=" O ASN O 236 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.064A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.625A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.160A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'M' and resid 25 through 26 Processing sheet with id=AB2, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.607A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N LYS M 60 " --> pdb=" O TRP M 69 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N TRP M 69 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N THR M 62 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 5.048A pdb=" N LEU M 67 " --> pdb=" O THR M 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'M' and resid 32 through 34 removed outlier: 3.607A pdb=" N GLU M 32 " --> pdb=" O SER M 137 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N TYR M 131 " --> pdb=" O ARG M 120 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N SER M 122 " --> pdb=" O LEU M 129 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU M 129 " --> pdb=" O SER M 122 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'M' and resid 40 through 43 Processing sheet with id=AB5, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.516A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LEU M 191 " --> pdb=" O TYR M 207 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N TYR M 207 " --> pdb=" O LEU M 191 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TRP M 193 " --> pdb=" O LEU M 205 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 168 through 171 removed outlier: 6.516A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR M 255 " --> pdb=" O GLN M 248 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 177 through 180 removed outlier: 3.795A pdb=" N ASP M 228 " --> pdb=" O SER M 225 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'N' and resid 25 through 26 Processing sheet with id=AB9, first strand: chain 'N' and resid 32 through 34 removed outlier: 6.500A pdb=" N ILE N 56 " --> pdb=" O TYR N 72 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N TYR N 72 " --> pdb=" O ILE N 56 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N TRP N 58 " --> pdb=" O ILE N 70 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'N' and resid 32 through 34 removed outlier: 3.854A pdb=" N TYR N 131 " --> pdb=" O ARG N 120 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N SER N 122 " --> pdb=" O LEU N 129 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LEU N 129 " --> pdb=" O SER N 122 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 40 through 43 Processing sheet with id=AC3, first strand: chain 'N' and resid 162 through 164 removed outlier: 3.829A pdb=" N VAL N 177 " --> pdb=" O ILE N 233 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE N 229 " --> pdb=" O CYS N 181 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ASP N 228 " --> pdb=" O SER N 225 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'N' and resid 168 through 171 removed outlier: 6.308A pdb=" N MET N 169 " --> pdb=" O GLU N 263 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'N' and resid 211 through 212 removed outlier: 6.454A pdb=" N TRP N 193 " --> pdb=" O LEU N 205 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU N 191 " --> pdb=" O TYR N 207 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 191 through 195 removed outlier: 4.149A pdb=" N VAL O 194 " --> pdb=" O THR O 200 " (cutoff:3.500A) removed outlier: 7.509A pdb=" N THR O 200 " --> pdb=" O VAL O 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN O 253 " --> pdb=" O LYS O 244 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS O 244 " --> pdb=" O GLN O 253 " (cutoff:3.500A) 567 hydrogen bonds defined for protein. 1587 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 680 hydrogen bond angles 0 basepair planarities 137 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 4.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1913 1.30 - 1.43: 5900 1.43 - 1.56: 8525 1.56 - 1.69: 562 1.69 - 1.82: 58 Bond restraints: 16958 Sorted by residual: bond pdb=" C HIS D 46 " pdb=" O HIS D 46 " ideal model delta sigma weight residual 1.238 1.173 0.064 1.08e-02 8.57e+03 3.56e+01 bond pdb=" C GLN E 125 " pdb=" O GLN E 125 " ideal model delta sigma weight residual 1.237 1.169 0.067 1.19e-02 7.06e+03 3.21e+01 bond pdb=" C ARG B 92 " pdb=" O ARG B 92 " ideal model delta sigma weight residual 1.236 1.169 0.067 1.29e-02 6.01e+03 2.67e+01 bond pdb=" CA ARG B 92 " pdb=" C ARG B 92 " ideal model delta sigma weight residual 1.522 1.458 0.065 1.40e-02 5.10e+03 2.13e+01 bond pdb=" C ARG B 92 " pdb=" N GLN B 93 " ideal model delta sigma weight residual 1.334 1.276 0.058 1.30e-02 5.92e+03 1.98e+01 ... (remaining 16953 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.25: 24092 7.25 - 14.50: 8 14.50 - 21.75: 0 21.75 - 29.00: 0 29.00 - 36.24: 1 Bond angle restraints: 24101 Sorted by residual: angle pdb=" C LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta sigma weight residual 109.80 73.56 36.24 1.23e+00 6.61e-01 8.68e+02 angle pdb=" O3' DC J 15 " pdb=" C3' DC J 15 " pdb=" C2' DC J 15 " ideal model delta sigma weight residual 111.50 97.89 13.61 1.50e+00 4.44e-01 8.24e+01 angle pdb=" C2' DC J 15 " pdb=" C1' DC J 15 " pdb=" N1 DC J 15 " ideal model delta sigma weight residual 113.50 100.09 13.41 1.50e+00 4.44e-01 8.00e+01 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" C LEU O 250 " ideal model delta sigma weight residual 111.74 122.51 -10.77 1.35e+00 5.49e-01 6.36e+01 angle pdb=" C2' DG J 72 " pdb=" C1' DG J 72 " pdb=" N9 DG J 72 " ideal model delta sigma weight residual 113.50 122.09 -8.59 1.50e+00 4.44e-01 3.28e+01 ... (remaining 24096 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.17: 7821 33.17 - 66.34: 1654 66.34 - 99.52: 37 99.52 - 132.69: 0 132.69 - 165.86: 2 Dihedral angle restraints: 9514 sinusoidal: 5738 harmonic: 3776 Sorted by residual: dihedral pdb=" C LYS O 249 " pdb=" N LYS O 249 " pdb=" CA LYS O 249 " pdb=" CB LYS O 249 " ideal model delta harmonic sigma weight residual -122.60 -80.21 -42.39 0 2.50e+00 1.60e-01 2.88e+02 dihedral pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual 122.80 151.15 -28.35 0 2.50e+00 1.60e-01 1.29e+02 dihedral pdb=" C LEU O 250 " pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta harmonic sigma weight residual -122.60 -148.59 25.99 0 2.50e+00 1.60e-01 1.08e+02 ... (remaining 9511 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2701 0.243 - 0.485: 4 0.485 - 0.728: 0 0.728 - 0.971: 0 0.971 - 1.213: 1 Chirality restraints: 2706 Sorted by residual: chirality pdb=" CA LEU O 250 " pdb=" N LEU O 250 " pdb=" C LEU O 250 " pdb=" CB LEU O 250 " both_signs ideal model delta sigma weight residual False 2.51 1.30 1.21 2.00e-01 2.50e+01 3.68e+01 chirality pdb=" CA LYS O 249 " pdb=" N LYS O 249 " pdb=" C LYS O 249 " pdb=" CB LYS O 249 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" C1' DG J 72 " pdb=" O4' DG J 72 " pdb=" C2' DG J 72 " pdb=" N9 DG J 72 " both_signs ideal model delta sigma weight residual False 2.42 2.08 0.34 2.00e-01 2.50e+01 2.87e+00 ... (remaining 2703 not shown) Planarity restraints: 2058 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 15 " -0.032 2.00e-02 2.50e+03 4.52e-02 4.60e+01 pdb=" N1 DC J 15 " -0.080 2.00e-02 2.50e+03 pdb=" C2 DC J 15 " 0.055 2.00e-02 2.50e+03 pdb=" O2 DC J 15 " 0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 15 " 0.010 2.00e-02 2.50e+03 pdb=" C4 DC J 15 " -0.007 2.00e-02 2.50e+03 pdb=" N4 DC J 15 " -0.033 2.00e-02 2.50e+03 pdb=" C5 DC J 15 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC J 15 " 0.081 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 147 " -0.034 2.00e-02 2.50e+03 1.88e-02 8.85e+00 pdb=" N1 DT I 147 " 0.027 2.00e-02 2.50e+03 pdb=" C2 DT I 147 " -0.005 2.00e-02 2.50e+03 pdb=" O2 DT I 147 " 0.029 2.00e-02 2.50e+03 pdb=" N3 DT I 147 " -0.023 2.00e-02 2.50e+03 pdb=" C4 DT I 147 " -0.011 2.00e-02 2.50e+03 pdb=" O4 DT I 147 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DT I 147 " 0.006 2.00e-02 2.50e+03 pdb=" C7 DT I 147 " 0.008 2.00e-02 2.50e+03 pdb=" C6 DT I 147 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 72 " -0.009 2.00e-02 2.50e+03 1.70e-02 8.62e+00 pdb=" N9 DG J 72 " 0.026 2.00e-02 2.50e+03 pdb=" C8 DG J 72 " 0.009 2.00e-02 2.50e+03 pdb=" N7 DG J 72 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 72 " 0.003 2.00e-02 2.50e+03 pdb=" C6 DG J 72 " 0.001 2.00e-02 2.50e+03 pdb=" O6 DG J 72 " -0.000 2.00e-02 2.50e+03 pdb=" N1 DG J 72 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DG J 72 " -0.026 2.00e-02 2.50e+03 pdb=" N2 DG J 72 " 0.031 2.00e-02 2.50e+03 pdb=" N3 DG J 72 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DG J 72 " -0.030 2.00e-02 2.50e+03 ... (remaining 2055 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 174 2.62 - 3.19: 12862 3.19 - 3.76: 28342 3.76 - 4.33: 39525 4.33 - 4.90: 57867 Nonbonded interactions: 138770 Sorted by model distance: nonbonded pdb=" O LYS O 249 " pdb=" CB LYS O 249 " model vdw 2.044 2.752 nonbonded pdb=" OG1 THR O 240 " pdb=" OE1 GLU O 242 " model vdw 2.165 3.040 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.200 3.120 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 3.120 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.235 3.120 ... (remaining 138765 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 38 through 133) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'M' selection = chain 'N' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.690 Check model and map are aligned: 0.130 Set scattering table: 0.190 Process input model: 42.520 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 16958 Z= 0.307 Angle : 0.718 36.245 24101 Z= 0.442 Chirality : 0.047 1.213 2706 Planarity : 0.004 0.045 2058 Dihedral : 26.463 165.860 7082 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.09 % Allowed : 25.20 % Favored : 74.71 % Cbeta Deviations : 0.25 % Peptide Plane: Cis-proline : 0.00 % 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: 1.34 (0.24), residues: 1275 helix: 2.22 (0.22), residues: 570 sheet: 0.25 (0.35), residues: 236 loop : -0.40 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP O 193 HIS 0.004 0.001 HIS D 46 PHE 0.025 0.002 PHE O 254 TYR 0.028 0.001 TYR O 175 ARG 0.011 0.000 ARG M 176 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 290 time to evaluate : 1.486 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 92 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8578 (mt-10) REVERT: D 32 GLU cc_start: 0.8462 (tm-30) cc_final: 0.8097 (tt0) REVERT: D 65 ASP cc_start: 0.8642 (t0) cc_final: 0.8350 (t0) REVERT: D 73 GLU cc_start: 0.8638 (tp30) cc_final: 0.8224 (tp30) REVERT: E 90 MET cc_start: 0.8647 (mmp) cc_final: 0.8424 (mmm) REVERT: E 115 LYS cc_start: 0.8778 (mttt) cc_final: 0.8538 (mttm) REVERT: F 59 LYS cc_start: 0.8729 (tttt) cc_final: 0.8497 (tptp) REVERT: G 59 THR cc_start: 0.9347 (t) cc_final: 0.9025 (m) REVERT: H 34 TYR cc_start: 0.9017 (m-80) cc_final: 0.8677 (m-80) REVERT: M 104 GLU cc_start: 0.8192 (tt0) cc_final: 0.7977 (tt0) REVERT: N 103 MET cc_start: 0.8796 (ttp) cc_final: 0.8476 (ttm) REVERT: N 111 GLU cc_start: 0.8766 (pp20) cc_final: 0.8362 (pp20) REVERT: N 112 ASP cc_start: 0.8407 (m-30) cc_final: 0.7980 (m-30) REVERT: N 180 THR cc_start: 0.8640 (m) cc_final: 0.8440 (p) REVERT: N 261 LYS cc_start: 0.8993 (mtpm) cc_final: 0.8723 (mtpp) REVERT: O 225 MET cc_start: -0.2950 (ptm) cc_final: -0.3850 (tmm) outliers start: 1 outliers final: 0 residues processed: 291 average time/residue: 1.8711 time to fit residues: 585.8554 Evaluate side-chains 210 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 210 time to evaluate : 1.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 115 optimal weight: 4.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 6.9990 chunk 46 optimal weight: 0.7980 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 2.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 60 ASN E 125 GLN F 93 GLN M 61 GLN N 28 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 16958 Z= 0.343 Angle : 0.643 9.079 24101 Z= 0.365 Chirality : 0.040 0.200 2706 Planarity : 0.005 0.048 2058 Dihedral : 28.648 164.712 4560 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 3.61 % Allowed : 23.85 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.32 (0.24), residues: 1275 helix: 2.21 (0.22), residues: 577 sheet: 0.27 (0.35), residues: 232 loop : -0.48 (0.29), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP O 193 HIS 0.004 0.001 HIS N 249 PHE 0.013 0.002 PHE O 254 TYR 0.018 0.002 TYR G 50 ARG 0.007 0.001 ARG O 214 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 1.457 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.6998 (tpp80) REVERT: C 91 GLU cc_start: 0.8549 (tt0) cc_final: 0.7835 (tt0) REVERT: C 92 GLU cc_start: 0.8831 (mt-10) cc_final: 0.8554 (mt-10) REVERT: D 64 ASN cc_start: 0.8811 (m-40) cc_final: 0.8598 (m-40) REVERT: D 73 GLU cc_start: 0.8710 (tp30) cc_final: 0.8377 (tp30) REVERT: D 90 GLU cc_start: 0.8891 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: E 115 LYS cc_start: 0.8769 (mttt) cc_final: 0.8529 (mttp) REVERT: F 35 ARG cc_start: 0.8005 (mtm110) cc_final: 0.7699 (mtp85) REVERT: F 91 LYS cc_start: 0.8931 (tttt) cc_final: 0.8436 (ttmm) REVERT: G 64 GLU cc_start: 0.8531 (tt0) cc_final: 0.8196 (tt0) REVERT: H 34 TYR cc_start: 0.9072 (m-80) cc_final: 0.8698 (m-80) REVERT: H 68 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7396 (tp30) REVERT: H 90 GLU cc_start: 0.8824 (OUTLIER) cc_final: 0.7535 (mp0) REVERT: M 103 MET cc_start: 0.9018 (OUTLIER) cc_final: 0.8735 (ttp) REVERT: M 104 GLU cc_start: 0.8397 (tt0) cc_final: 0.8007 (tt0) REVERT: M 130 ASP cc_start: 0.8680 (p0) cc_final: 0.8471 (p0) REVERT: M 163 THR cc_start: 0.8548 (m) cc_final: 0.8207 (p) REVERT: M 219 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8108 (ttp80) REVERT: M 235 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7255 (t0) REVERT: M 237 GLU cc_start: 0.8108 (mm-30) cc_final: 0.7394 (mm-30) REVERT: N 32 GLU cc_start: 0.8155 (mm-30) cc_final: 0.7699 (mm-30) REVERT: N 103 MET cc_start: 0.8829 (OUTLIER) cc_final: 0.8502 (ttm) REVERT: N 111 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.8325 (pp20) REVERT: N 112 ASP cc_start: 0.8472 (m-30) cc_final: 0.7999 (m-30) REVERT: N 261 LYS cc_start: 0.9120 (mtpm) cc_final: 0.8891 (mtpp) REVERT: O 225 MET cc_start: -0.2553 (ptm) cc_final: -0.3468 (tmm) outliers start: 40 outliers final: 11 residues processed: 235 average time/residue: 1.8212 time to fit residues: 461.0006 Evaluate side-chains 221 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 1.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 93 THR Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 chunk 114 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 149 optimal weight: 4.9990 chunk 123 optimal weight: 0.1980 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 110 optimal weight: 1.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.2755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16958 Z= 0.200 Angle : 0.569 8.799 24101 Z= 0.328 Chirality : 0.036 0.193 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.475 166.030 4560 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 3.25 % Allowed : 24.21 % Favored : 72.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.59 (0.24), residues: 1275 helix: 2.45 (0.21), residues: 578 sheet: 0.43 (0.35), residues: 232 loop : -0.39 (0.29), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.003 0.001 HIS B 75 PHE 0.020 0.001 PHE O 254 TYR 0.011 0.001 TYR G 50 ARG 0.005 0.000 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 208 time to evaluate : 1.626 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8204 (OUTLIER) cc_final: 0.7250 (ttp80) REVERT: A 133 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: B 25 ASN cc_start: 0.8726 (m-40) cc_final: 0.8375 (m-40) REVERT: C 91 GLU cc_start: 0.8549 (tt0) cc_final: 0.7850 (tt0) REVERT: C 92 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8567 (mt-10) REVERT: D 44 GLN cc_start: 0.8083 (tt0) cc_final: 0.7604 (mt0) REVERT: D 73 GLU cc_start: 0.8615 (tp30) cc_final: 0.8383 (tp30) REVERT: D 90 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.7799 (mt-10) REVERT: E 97 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7816 (mt-10) REVERT: E 115 LYS cc_start: 0.8713 (mttt) cc_final: 0.8485 (mttp) REVERT: E 123 ASP cc_start: 0.8952 (m-30) cc_final: 0.8750 (m-30) REVERT: F 91 LYS cc_start: 0.8909 (tttt) cc_final: 0.8446 (ttmm) REVERT: H 34 TYR cc_start: 0.9024 (m-80) cc_final: 0.8611 (m-80) REVERT: H 68 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7368 (tp30) REVERT: H 90 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.7495 (mp0) REVERT: M 103 MET cc_start: 0.9040 (OUTLIER) cc_final: 0.8781 (ttp) REVERT: M 104 GLU cc_start: 0.8376 (tt0) cc_final: 0.8161 (tt0) REVERT: M 163 THR cc_start: 0.8530 (m) cc_final: 0.8223 (p) REVERT: M 219 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8396 (ttp80) REVERT: M 235 ASN cc_start: 0.8078 (OUTLIER) cc_final: 0.7385 (t0) REVERT: M 237 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7564 (mm-30) REVERT: N 32 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7764 (mm-30) REVERT: N 103 MET cc_start: 0.8738 (OUTLIER) cc_final: 0.8455 (ttm) REVERT: N 111 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8421 (pp20) REVERT: N 112 ASP cc_start: 0.8372 (m-30) cc_final: 0.7944 (m-30) REVERT: O 198 LYS cc_start: -0.1967 (OUTLIER) cc_final: -0.2479 (ptmt) REVERT: O 225 MET cc_start: -0.2409 (ptm) cc_final: -0.3268 (tmm) outliers start: 36 outliers final: 13 residues processed: 230 average time/residue: 1.7353 time to fit residues: 431.7998 Evaluate side-chains 225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 1.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 198 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 8.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 15 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN A 108 ASN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.3079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 16958 Z= 0.277 Angle : 0.598 8.859 24101 Z= 0.341 Chirality : 0.037 0.188 2706 Planarity : 0.004 0.043 2058 Dihedral : 28.643 164.730 4560 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.16 % Allowed : 23.49 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.24), residues: 1275 helix: 2.25 (0.21), residues: 577 sheet: 0.52 (0.36), residues: 230 loop : -0.50 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.002 TYR G 50 ARG 0.008 0.001 ARG E 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 211 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7105 (tpp80) REVERT: A 133 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7841 (mt-10) REVERT: B 25 ASN cc_start: 0.8904 (m-40) cc_final: 0.8457 (m-40) REVERT: B 92 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8140 (ttp80) REVERT: C 20 ARG cc_start: 0.8557 (mtt-85) cc_final: 0.8318 (mtt-85) REVERT: C 71 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7926 (ttp80) REVERT: C 91 GLU cc_start: 0.8602 (tt0) cc_final: 0.7966 (tt0) REVERT: C 92 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8523 (mt-10) REVERT: D 44 GLN cc_start: 0.8035 (tt0) cc_final: 0.7673 (mt0) REVERT: D 90 GLU cc_start: 0.8893 (OUTLIER) cc_final: 0.7735 (mt-10) REVERT: E 97 GLU cc_start: 0.8018 (mm-30) cc_final: 0.7791 (mt-10) REVERT: E 115 LYS cc_start: 0.8759 (mttt) cc_final: 0.8524 (mttp) REVERT: F 91 LYS cc_start: 0.8923 (tttt) cc_final: 0.8429 (ttmm) REVERT: G 51 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.7835 (tpt) REVERT: H 32 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.8063 (tt0) REVERT: H 34 TYR cc_start: 0.9072 (m-80) cc_final: 0.8704 (m-80) REVERT: H 68 GLU cc_start: 0.7609 (OUTLIER) cc_final: 0.7379 (tp30) REVERT: H 90 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.7499 (mp0) REVERT: M 103 MET cc_start: 0.9058 (OUTLIER) cc_final: 0.8736 (ttp) REVERT: M 104 GLU cc_start: 0.8486 (tt0) cc_final: 0.8209 (tt0) REVERT: M 235 ASN cc_start: 0.8131 (OUTLIER) cc_final: 0.7505 (t0) REVERT: M 237 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7535 (mm-30) REVERT: N 23 GLU cc_start: 0.6341 (OUTLIER) cc_final: 0.5506 (tp30) REVERT: N 32 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7745 (mm-30) REVERT: N 42 MET cc_start: 0.9066 (ptp) cc_final: 0.8754 (mpp) REVERT: N 103 MET cc_start: 0.8756 (ttp) cc_final: 0.8495 (ttm) REVERT: N 111 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8365 (pp20) REVERT: N 112 ASP cc_start: 0.8339 (m-30) cc_final: 0.7975 (m-30) REVERT: N 240 ASP cc_start: 0.8685 (m-30) cc_final: 0.8220 (m-30) REVERT: O 198 LYS cc_start: -0.2107 (OUTLIER) cc_final: -0.2665 (ptmt) REVERT: O 225 MET cc_start: -0.2393 (ptm) cc_final: -0.2920 (tmm) outliers start: 46 outliers final: 21 residues processed: 236 average time/residue: 1.7373 time to fit residues: 442.6820 Evaluate side-chains 235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0170 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 109 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 5.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 overall best weight: 1.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 38 ASN E 108 ASN F 93 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 16958 Z= 0.279 Angle : 0.588 8.816 24101 Z= 0.337 Chirality : 0.037 0.178 2706 Planarity : 0.004 0.034 2058 Dihedral : 28.646 165.275 4560 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.34 % Allowed : 23.67 % Favored : 72.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.40 (0.24), residues: 1275 helix: 2.24 (0.21), residues: 576 sheet: 0.55 (0.36), residues: 232 loop : -0.53 (0.28), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.011 0.002 PHE A 67 TYR 0.014 0.001 TYR E 54 ARG 0.009 0.001 ARG N 188 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 1.556 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.7102 (tpp80) REVERT: B 25 ASN cc_start: 0.8860 (m-40) cc_final: 0.8408 (m-40) REVERT: B 92 ARG cc_start: 0.8745 (OUTLIER) cc_final: 0.8173 (ttp80) REVERT: C 91 GLU cc_start: 0.8618 (tt0) cc_final: 0.7982 (tt0) REVERT: C 92 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8533 (mt-10) REVERT: D 44 GLN cc_start: 0.8028 (tt0) cc_final: 0.7668 (mt0) REVERT: D 90 GLU cc_start: 0.8871 (OUTLIER) cc_final: 0.7750 (mt-10) REVERT: E 97 GLU cc_start: 0.8040 (mm-30) cc_final: 0.7825 (mt-10) REVERT: F 91 LYS cc_start: 0.8932 (tttt) cc_final: 0.8432 (ttmm) REVERT: G 72 ASP cc_start: 0.8469 (t0) cc_final: 0.8264 (t0) REVERT: H 34 TYR cc_start: 0.9039 (m-80) cc_final: 0.8646 (m-80) REVERT: H 68 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7378 (tp30) REVERT: H 90 GLU cc_start: 0.8845 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: M 103 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8755 (ttp) REVERT: M 104 GLU cc_start: 0.8480 (tt0) cc_final: 0.8204 (tt0) REVERT: N 23 GLU cc_start: 0.6358 (OUTLIER) cc_final: 0.5538 (tp30) REVERT: N 42 MET cc_start: 0.8977 (ptp) cc_final: 0.8682 (mpp) REVERT: N 103 MET cc_start: 0.8747 (ttp) cc_final: 0.8546 (ttm) REVERT: N 111 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8366 (pp20) REVERT: N 112 ASP cc_start: 0.8368 (m-30) cc_final: 0.7999 (m-30) REVERT: O 198 LYS cc_start: -0.2012 (OUTLIER) cc_final: -0.2574 (ptmt) REVERT: O 225 MET cc_start: -0.2341 (ptm) cc_final: -0.2908 (tmm) outliers start: 48 outliers final: 25 residues processed: 221 average time/residue: 1.6826 time to fit residues: 402.7858 Evaluate side-chains 227 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 193 time to evaluate : 1.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 246 VAL Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9990 chunk 132 optimal weight: 0.7980 chunk 29 optimal weight: 7.9990 chunk 86 optimal weight: 60.0000 chunk 36 optimal weight: 5.9990 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 0.1980 chunk 68 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 46 HIS G 104 GLN H 46 HIS ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8128 moved from start: 0.3449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16958 Z= 0.197 Angle : 0.564 8.962 24101 Z= 0.325 Chirality : 0.035 0.174 2706 Planarity : 0.004 0.039 2058 Dihedral : 28.480 165.650 4560 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.98 % Allowed : 25.29 % Favored : 71.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.62 (0.24), residues: 1275 helix: 2.45 (0.21), residues: 578 sheet: 0.59 (0.36), residues: 232 loop : -0.44 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.005 0.001 HIS H 46 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR E 54 ARG 0.011 0.000 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 210 time to evaluate : 1.312 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 129 ARG cc_start: 0.8207 (OUTLIER) cc_final: 0.7108 (tpp80) REVERT: A 133 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.8002 (mt-10) REVERT: B 25 ASN cc_start: 0.8861 (m-40) cc_final: 0.8446 (m-40) REVERT: C 91 GLU cc_start: 0.8602 (tt0) cc_final: 0.8004 (tt0) REVERT: C 92 GLU cc_start: 0.8803 (mt-10) cc_final: 0.8552 (mt-10) REVERT: D 44 GLN cc_start: 0.8064 (tt0) cc_final: 0.7728 (mt0) REVERT: D 90 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: F 77 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8594 (mttt) REVERT: F 91 LYS cc_start: 0.8918 (tttt) cc_final: 0.8418 (ttmm) REVERT: G 51 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7696 (tpt) REVERT: H 34 TYR cc_start: 0.9005 (m-80) cc_final: 0.8591 (m-80) REVERT: H 68 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7330 (tp30) REVERT: H 90 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: M 103 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8710 (ttp) REVERT: M 104 GLU cc_start: 0.8431 (tt0) cc_final: 0.8165 (tt0) REVERT: M 219 ARG cc_start: 0.8872 (mtm110) cc_final: 0.8227 (ttp80) REVERT: N 32 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7733 (mt-10) REVERT: N 109 THR cc_start: 0.7893 (OUTLIER) cc_final: 0.7460 (t) REVERT: N 111 GLU cc_start: 0.8681 (OUTLIER) cc_final: 0.8284 (pp20) REVERT: N 240 ASP cc_start: 0.8437 (m-30) cc_final: 0.7999 (m-30) REVERT: O 198 LYS cc_start: -0.2125 (OUTLIER) cc_final: -0.2682 (ptmt) outliers start: 33 outliers final: 16 residues processed: 231 average time/residue: 1.6559 time to fit residues: 414.6458 Evaluate side-chains 230 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 203 time to evaluate : 1.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 109 THR Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 20.0000 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN D 46 HIS D 92 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 104 GLN N 61 GLN N 196 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.083 16958 Z= 0.579 Angle : 0.711 9.049 24101 Z= 0.399 Chirality : 0.045 0.170 2706 Planarity : 0.006 0.041 2058 Dihedral : 29.264 161.186 4560 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.88 % Allowed : 24.57 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.90 (0.23), residues: 1275 helix: 1.78 (0.21), residues: 573 sheet: 0.39 (0.35), residues: 232 loop : -0.76 (0.27), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP O 193 HIS 0.005 0.001 HIS M 249 PHE 0.015 0.003 PHE M 256 TYR 0.020 0.002 TYR E 54 ARG 0.012 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 203 time to evaluate : 1.549 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8409 (mm-30) cc_final: 0.8167 (mt-10) REVERT: A 133 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7787 (mt-10) REVERT: C 91 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8130 (tt0) REVERT: D 39 TYR cc_start: 0.7953 (t80) cc_final: 0.7622 (t80) REVERT: D 44 GLN cc_start: 0.8167 (tt0) cc_final: 0.7739 (mt0) REVERT: D 90 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.7839 (mp0) REVERT: F 91 LYS cc_start: 0.8954 (tttt) cc_final: 0.8496 (ttmm) REVERT: H 32 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8107 (tt0) REVERT: H 34 TYR cc_start: 0.9118 (m-80) cc_final: 0.8750 (m-80) REVERT: H 68 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7418 (tp30) REVERT: H 90 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.7724 (mp0) REVERT: M 81 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8045 (ttpt) REVERT: M 103 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8709 (ttp) REVERT: M 104 GLU cc_start: 0.8479 (tt0) cc_final: 0.8164 (tt0) REVERT: M 235 ASN cc_start: 0.8382 (OUTLIER) cc_final: 0.7862 (t0) REVERT: M 237 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7849 (mm-30) REVERT: N 23 GLU cc_start: 0.6500 (OUTLIER) cc_final: 0.5695 (tp30) REVERT: N 32 GLU cc_start: 0.8251 (mm-30) cc_final: 0.7743 (mt-10) REVERT: N 111 GLU cc_start: 0.8770 (OUTLIER) cc_final: 0.8328 (pp20) REVERT: N 112 ASP cc_start: 0.8481 (m-30) cc_final: 0.8126 (m-30) REVERT: O 198 LYS cc_start: -0.2423 (OUTLIER) cc_final: -0.2960 (ptmt) outliers start: 43 outliers final: 22 residues processed: 229 average time/residue: 1.8106 time to fit residues: 446.9932 Evaluate side-chains 235 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 201 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 99 LYS Chi-restraints excluded: chain H residue 32 GLU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 0.5980 chunk 28 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 0.6980 chunk 115 optimal weight: 0.5980 chunk 133 optimal weight: 0.9990 chunk 140 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 76 GLN C 104 GLN D 46 HIS F 93 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 moved from start: 0.3785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 16958 Z= 0.187 Angle : 0.585 8.920 24101 Z= 0.335 Chirality : 0.035 0.169 2706 Planarity : 0.004 0.038 2058 Dihedral : 28.547 162.566 4560 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.07 % Allowed : 25.56 % Favored : 71.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.42 (0.24), residues: 1275 helix: 2.32 (0.21), residues: 577 sheet: 0.47 (0.36), residues: 232 loop : -0.57 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.012 0.001 PHE A 67 TYR 0.015 0.001 TYR E 54 ARG 0.010 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 204 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 GLU cc_start: 0.8209 (mm-30) cc_final: 0.7989 (mt-10) REVERT: A 133 GLU cc_start: 0.8198 (OUTLIER) cc_final: 0.7892 (mt-10) REVERT: B 25 ASN cc_start: 0.8879 (m-40) cc_final: 0.8524 (m-40) REVERT: C 71 ARG cc_start: 0.7945 (ttp80) cc_final: 0.7646 (ttp80) REVERT: C 91 GLU cc_start: 0.8601 (tt0) cc_final: 0.8041 (tt0) REVERT: D 44 GLN cc_start: 0.8003 (tt0) cc_final: 0.7632 (mt0) REVERT: D 90 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: F 91 LYS cc_start: 0.8906 (tttt) cc_final: 0.8455 (ttmm) REVERT: H 34 TYR cc_start: 0.8974 (m-80) cc_final: 0.8607 (m-80) REVERT: H 68 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7380 (tp30) REVERT: H 90 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7493 (mp0) REVERT: M 103 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8673 (ttp) REVERT: M 104 GLU cc_start: 0.8468 (tt0) cc_final: 0.8139 (tt0) REVERT: N 32 GLU cc_start: 0.8231 (mm-30) cc_final: 0.7714 (mt-10) REVERT: N 109 THR cc_start: 0.8024 (m) cc_final: 0.7807 (t) REVERT: N 111 GLU cc_start: 0.8769 (pp20) cc_final: 0.8371 (pp20) REVERT: O 198 LYS cc_start: -0.2106 (OUTLIER) cc_final: -0.2643 (ptmt) outliers start: 34 outliers final: 19 residues processed: 225 average time/residue: 1.6970 time to fit residues: 412.8914 Evaluate side-chains 225 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 200 time to evaluate : 1.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 140 VAL Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 225 MET Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0050 chunk 136 optimal weight: 5.9990 chunk 140 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.3980 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 4.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN F 93 GLN G 104 GLN N 61 GLN N 196 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 253 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 16958 Z= 0.171 Angle : 0.576 9.233 24101 Z= 0.330 Chirality : 0.035 0.168 2706 Planarity : 0.004 0.045 2058 Dihedral : 28.384 162.854 4560 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.44 % Allowed : 26.29 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.64 (0.24), residues: 1275 helix: 2.55 (0.21), residues: 577 sheet: 0.44 (0.35), residues: 232 loop : -0.45 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.004 0.001 HIS B 75 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.001 TYR E 54 ARG 0.014 0.001 ARG A 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 202 time to evaluate : 1.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8883 (m-40) cc_final: 0.8530 (m-40) REVERT: C 91 GLU cc_start: 0.8607 (tt0) cc_final: 0.8116 (tt0) REVERT: D 44 GLN cc_start: 0.8020 (tt0) cc_final: 0.7695 (mt0) REVERT: D 90 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8471 (mp0) REVERT: F 77 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8699 (mttt) REVERT: F 91 LYS cc_start: 0.8895 (tttt) cc_final: 0.8402 (ttmm) REVERT: H 34 TYR cc_start: 0.8958 (m-80) cc_final: 0.8575 (m-80) REVERT: H 68 GLU cc_start: 0.7600 (OUTLIER) cc_final: 0.7340 (tp30) REVERT: M 104 GLU cc_start: 0.8428 (tt0) cc_final: 0.8224 (tt0) REVERT: N 32 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7687 (mt-10) REVERT: N 109 THR cc_start: 0.8036 (m) cc_final: 0.7763 (t) REVERT: N 111 GLU cc_start: 0.8793 (OUTLIER) cc_final: 0.8485 (pp20) REVERT: N 112 ASP cc_start: 0.7934 (m-30) cc_final: 0.7663 (m-30) REVERT: N 240 ASP cc_start: 0.8466 (m-30) cc_final: 0.8077 (m-30) REVERT: O 198 LYS cc_start: -0.2223 (OUTLIER) cc_final: -0.2755 (ptmt) outliers start: 27 outliers final: 13 residues processed: 216 average time/residue: 1.7517 time to fit residues: 408.3456 Evaluate side-chains 215 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 197 time to evaluate : 1.498 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 177 VAL Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 225 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 7.9990 chunk 68 optimal weight: 0.0370 chunk 100 optimal weight: 0.0030 chunk 151 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 3.9990 overall best weight: 0.5470 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 253 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 16958 Z= 0.173 Angle : 0.579 9.452 24101 Z= 0.331 Chirality : 0.035 0.168 2706 Planarity : 0.004 0.046 2058 Dihedral : 28.354 162.805 4560 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 1.90 % Allowed : 27.10 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.24), residues: 1275 helix: 2.58 (0.21), residues: 577 sheet: 0.47 (0.35), residues: 232 loop : -0.42 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.011 0.001 PHE O 254 TYR 0.014 0.001 TYR E 54 ARG 0.018 0.001 ARG A 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2550 Ramachandran restraints generated. 1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 1.479 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8911 (m-40) cc_final: 0.8512 (m-40) REVERT: C 91 GLU cc_start: 0.8604 (tt0) cc_final: 0.8107 (tt0) REVERT: D 44 GLN cc_start: 0.8056 (tt0) cc_final: 0.7702 (mt0) REVERT: D 90 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.7804 (mt-10) REVERT: F 77 LYS cc_start: 0.8909 (OUTLIER) cc_final: 0.8702 (mttt) REVERT: F 91 LYS cc_start: 0.8896 (tttt) cc_final: 0.8406 (ttmm) REVERT: H 34 TYR cc_start: 0.8947 (m-80) cc_final: 0.8553 (m-80) REVERT: H 68 GLU cc_start: 0.7603 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: M 104 GLU cc_start: 0.8439 (tt0) cc_final: 0.8223 (tt0) REVERT: N 32 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7691 (mt-10) REVERT: N 109 THR cc_start: 0.8056 (m) cc_final: 0.7770 (t) REVERT: N 111 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8493 (pp20) REVERT: N 112 ASP cc_start: 0.7898 (m-30) cc_final: 0.7634 (m-30) REVERT: N 240 ASP cc_start: 0.8436 (m-30) cc_final: 0.8163 (m-30) REVERT: O 198 LYS cc_start: -0.2112 (OUTLIER) cc_final: -0.2610 (ptmt) outliers start: 21 outliers final: 13 residues processed: 215 average time/residue: 1.8347 time to fit residues: 426.6649 Evaluate side-chains 218 residues out of total 1110 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 200 time to evaluate : 1.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 90 GLU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 77 LYS Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain N residue 111 GLU Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 165 SER Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Chi-restraints excluded: chain O residue 198 LYS Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 225 MET Chi-restraints excluded: chain O residue 253 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 120 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.105472 restraints weight = 20749.496| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.00 r_work: 0.2978 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.133 16958 Z= 0.245 Angle : 0.778 59.199 24101 Z= 0.454 Chirality : 0.036 0.321 2706 Planarity : 0.004 0.044 2058 Dihedral : 28.353 162.808 4560 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.72 % Allowed : 27.64 % Favored : 70.64 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 0.00 % 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: 1.68 (0.24), residues: 1275 helix: 2.57 (0.21), residues: 577 sheet: 0.47 (0.35), residues: 232 loop : -0.41 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.014 0.001 PHE O 254 TYR 0.014 0.001 TYR E 54 ARG 0.018 0.001 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6875.08 seconds wall clock time: 123 minutes 22.10 seconds (7402.10 seconds total)