Starting phenix.real_space_refine on Fri Feb 16 17:57:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/02_2024/8evh_28629.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/02_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_28629/02_2024/8evh_28629.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/02_2024/8evh_28629.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/02_2024/8evh_28629.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evh_28629/02_2024/8evh_28629.pdb" } 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 Residue "B GLU 52": "OE1" <-> "OE2" Residue "D GLU 32": "OE1" <-> "OE2" Residue "D GLU 90": "OE1" <-> "OE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "M GLU 111": "OE1" <-> "OE2" Residue "N TYR 245": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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 - 3.50 Amino acid : False - 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: 7.61 Conformation dependent library (CDL) restraints added in 1.9 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: 7.39 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: 6.28 Time building geometry restraints manager: 8.09 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: 73.56 - 85.65: 1 85.65 - 97.75: 1 97.75 - 109.85: 5054 109.85 - 121.95: 15439 121.95 - 134.05: 3606 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 2.440 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.200 2.520 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 2.520 nonbonded pdb=" N GLU B 52 " pdb=" OE1 GLU B 52 " model vdw 2.235 2.520 ... (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 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: 0.650 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: 0.010 Extract box with map and model: 3.740 Check model and map are aligned: 0.220 Set scattering table: 0.140 Process input model: 50.300 Find NCS groups from input model: 0.670 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:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.210 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 290 time to evaluate : 1.593 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: 1.7748 time to fit residues: 554.8093 Evaluate side-chains 210 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 1.292 ------------------------------------------------------------------------------- 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: 5.9990 chunk 39 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 119 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 10.0000 chunk 88 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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 195 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: 0.8104 moved from start: 0.2033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16958 Z= 0.238 Angle : 0.598 9.287 24101 Z= 0.343 Chirality : 0.037 0.202 2706 Planarity : 0.004 0.042 2058 Dihedral : 28.424 166.170 4560 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.25 % Allowed : 24.75 % 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: 1.55 (0.24), residues: 1275 helix: 2.42 (0.22), residues: 578 sheet: 0.37 (0.35), residues: 236 loop : -0.42 (0.29), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP O 193 HIS 0.003 0.001 HIS F 75 PHE 0.013 0.002 PHE O 254 TYR 0.014 0.002 TYR G 50 ARG 0.008 0.001 ARG F 35 *********************** 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 247 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 211 time to evaluate : 1.520 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8344 (tttp) REVERT: C 92 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8535 (mt-10) REVERT: D 32 GLU cc_start: 0.8447 (tm-30) cc_final: 0.7856 (tm-30) REVERT: D 64 ASN cc_start: 0.8788 (m-40) cc_final: 0.8586 (m-40) REVERT: D 73 GLU cc_start: 0.8662 (tp30) cc_final: 0.8334 (tp30) REVERT: E 115 LYS cc_start: 0.8735 (mttt) cc_final: 0.8493 (mttp) REVERT: F 35 ARG cc_start: 0.7894 (mtm110) cc_final: 0.7673 (mtp85) REVERT: H 34 TYR cc_start: 0.9025 (m-80) cc_final: 0.8646 (m-80) REVERT: H 68 GLU cc_start: 0.7615 (OUTLIER) cc_final: 0.7407 (tp30) REVERT: H 90 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.7297 (mp0) REVERT: M 104 GLU cc_start: 0.8365 (tt0) cc_final: 0.8029 (tt0) REVERT: M 163 THR cc_start: 0.8500 (m) cc_final: 0.8227 (p) REVERT: M 235 ASN cc_start: 0.8022 (OUTLIER) cc_final: 0.7716 (t0) REVERT: M 237 GLU cc_start: 0.8042 (mm-30) cc_final: 0.7359 (mm-30) REVERT: N 32 GLU cc_start: 0.8152 (mm-30) cc_final: 0.7753 (mm-30) REVERT: N 103 MET cc_start: 0.8843 (OUTLIER) cc_final: 0.8496 (ttm) REVERT: N 111 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8301 (pp20) REVERT: N 112 ASP cc_start: 0.8462 (m-30) cc_final: 0.8000 (m-30) REVERT: N 261 LYS cc_start: 0.9093 (mtpm) cc_final: 0.8840 (mtpp) REVERT: O 225 MET cc_start: -0.2463 (ptm) cc_final: -0.3216 (tmm) outliers start: 36 outliers final: 12 residues processed: 234 average time/residue: 1.6530 time to fit residues: 418.0780 Evaluate side-chains 223 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 205 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 139 THR Chi-restraints excluded: chain M residue 172 SER 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: 0.4980 chunk 93 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 138 optimal weight: 5.9990 chunk 149 optimal weight: 0.9980 chunk 123 optimal weight: 0.0770 chunk 137 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 110 optimal weight: 5.9990 overall best weight: 0.6940 ------------------------------------------------------------------------------- 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: 0.8080 moved from start: 0.2504 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= 0.172 Angle : 0.550 8.803 24101 Z= 0.318 Chirality : 0.035 0.199 2706 Planarity : 0.004 0.040 2058 Dihedral : 28.311 167.172 4560 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.62 % Allowed : 26.02 % 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: 1.73 (0.24), residues: 1275 helix: 2.61 (0.21), residues: 578 sheet: 0.43 (0.35), residues: 232 loop : -0.35 (0.28), residues: 465 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.003 0.001 HIS B 75 PHE 0.009 0.001 PHE A 67 TYR 0.011 0.001 TYR O 252 ARG 0.004 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 241 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 212 time to evaluate : 1.447 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8580 (OUTLIER) cc_final: 0.8266 (tttp) REVERT: C 91 GLU cc_start: 0.8536 (tt0) cc_final: 0.7853 (tt0) REVERT: C 92 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8501 (mt-10) REVERT: D 44 GLN cc_start: 0.8100 (tt0) cc_final: 0.7857 (tt0) REVERT: D 64 ASN cc_start: 0.8767 (m-40) cc_final: 0.8559 (m-40) REVERT: E 115 LYS cc_start: 0.8695 (mttt) cc_final: 0.8455 (mttp) REVERT: F 35 ARG cc_start: 0.7965 (mtm110) cc_final: 0.7711 (mtp85) REVERT: G 95 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8350 (ttpt) REVERT: H 34 TYR cc_start: 0.8980 (m-80) cc_final: 0.8601 (m-80) REVERT: H 68 GLU cc_start: 0.7667 (OUTLIER) cc_final: 0.7413 (tp30) REVERT: H 90 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.7259 (mp0) REVERT: M 104 GLU cc_start: 0.8336 (tt0) cc_final: 0.8041 (tt0) REVERT: M 163 THR cc_start: 0.8506 (m) cc_final: 0.8305 (p) REVERT: M 235 ASN cc_start: 0.8016 (OUTLIER) cc_final: 0.7594 (t0) REVERT: M 237 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7361 (mm-30) REVERT: N 32 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7795 (mm-30) REVERT: N 103 MET cc_start: 0.8742 (OUTLIER) cc_final: 0.8378 (ttm) REVERT: N 111 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8405 (pp20) REVERT: N 112 ASP cc_start: 0.8383 (m-30) cc_final: 0.7929 (m-30) REVERT: N 186 ASP cc_start: 0.9037 (OUTLIER) cc_final: 0.8806 (t70) REVERT: N 261 LYS cc_start: 0.9042 (mtpm) cc_final: 0.8798 (mtpp) REVERT: O 225 MET cc_start: -0.2155 (ptm) cc_final: -0.3032 (tmm) outliers start: 29 outliers final: 9 residues processed: 228 average time/residue: 1.6393 time to fit residues: 405.7984 Evaluate side-chains 218 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 201 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS Chi-restraints excluded: chain H residue 68 GLU 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 100 THR Chi-restraints excluded: chain M residue 138 VAL 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 186 ASP Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 246 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 138 optimal weight: 0.9990 chunk 146 optimal weight: 50.0000 chunk 72 optimal weight: 10.0000 chunk 131 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 60 ASN D 92 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16958 Z= 0.236 Angle : 0.570 8.956 24101 Z= 0.326 Chirality : 0.036 0.191 2706 Planarity : 0.004 0.043 2058 Dihedral : 28.486 166.072 4560 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.61 % Allowed : 24.75 % Favored : 71.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.63 (0.24), residues: 1275 helix: 2.48 (0.21), residues: 577 sheet: 0.46 (0.35), residues: 230 loop : -0.37 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.004 0.001 HIS N 249 PHE 0.012 0.001 PHE O 254 TYR 0.012 0.001 TYR G 50 ARG 0.008 0.000 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 240 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 1.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8626 (OUTLIER) cc_final: 0.8399 (tttp) REVERT: C 71 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7904 (ttp80) REVERT: C 91 GLU cc_start: 0.8573 (tt0) cc_final: 0.7906 (tt0) REVERT: D 44 GLN cc_start: 0.8113 (tt0) cc_final: 0.7709 (mt0) REVERT: D 64 ASN cc_start: 0.8802 (m-40) cc_final: 0.8589 (m-40) REVERT: D 90 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.7767 (mt-10) REVERT: E 115 LYS cc_start: 0.8717 (mttt) cc_final: 0.8490 (mttp) REVERT: G 95 LYS cc_start: 0.8847 (OUTLIER) cc_final: 0.8347 (ttpt) REVERT: H 34 TYR cc_start: 0.9075 (m-80) cc_final: 0.8675 (m-80) REVERT: H 68 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: H 90 GLU cc_start: 0.8782 (OUTLIER) cc_final: 0.7389 (mp0) REVERT: M 163 THR cc_start: 0.8539 (m) cc_final: 0.8237 (p) REVERT: M 175 GLU cc_start: 0.7386 (pt0) cc_final: 0.7082 (pm20) REVERT: M 235 ASN cc_start: 0.8076 (OUTLIER) cc_final: 0.7859 (t0) REVERT: N 32 GLU cc_start: 0.8187 (mm-30) cc_final: 0.7657 (mm-30) REVERT: N 103 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.8465 (ttm) REVERT: N 111 GLU cc_start: 0.8698 (pp20) cc_final: 0.8438 (pp20) REVERT: N 261 LYS cc_start: 0.9030 (mtpm) cc_final: 0.8801 (mtpp) REVERT: O 198 LYS cc_start: -0.2008 (OUTLIER) cc_final: -0.2576 (ptmt) REVERT: O 225 MET cc_start: -0.2298 (ptm) cc_final: -0.2641 (tmm) outliers start: 40 outliers final: 21 residues processed: 226 average time/residue: 1.5381 time to fit residues: 377.4357 Evaluate side-chains 215 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 185 time to evaluate : 1.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 62 ILE 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 E residue 87 SER Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS 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 H residue 109 SER Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 103 MET 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 211 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.2980 chunk 83 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 60 optimal weight: 1.9990 chunk 125 optimal weight: 2.9990 chunk 101 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- 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 ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.3129 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 : 0.550 8.972 24101 Z= 0.316 Chirality : 0.035 0.182 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.334 166.641 4560 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 25.29 % 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: 1.70 (0.24), residues: 1275 helix: 2.56 (0.21), residues: 578 sheet: 0.49 (0.35), residues: 230 loop : -0.36 (0.29), residues: 467 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.003 0.001 HIS F 75 PHE 0.010 0.001 PHE A 67 TYR 0.012 0.001 TYR E 54 ARG 0.011 0.000 ARG A 42 *********************** 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 231 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 193 time to evaluate : 1.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8343 (tttp) REVERT: B 92 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8158 (ttp80) REVERT: C 71 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7906 (ttp80) REVERT: C 91 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8005 (tt0) REVERT: D 44 GLN cc_start: 0.8039 (tt0) cc_final: 0.7659 (mt0) REVERT: D 64 ASN cc_start: 0.8795 (m-40) cc_final: 0.8585 (m-40) REVERT: E 115 LYS cc_start: 0.8698 (mttt) cc_final: 0.8469 (mttp) REVERT: G 51 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7710 (tpt) REVERT: G 95 LYS cc_start: 0.8855 (OUTLIER) cc_final: 0.8375 (ttpt) REVERT: H 34 TYR cc_start: 0.9023 (m-80) cc_final: 0.8641 (m-80) REVERT: H 68 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7342 (tp30) REVERT: H 90 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.7303 (mp0) REVERT: H 113 LYS cc_start: 0.8848 (ttpt) cc_final: 0.8502 (ttpt) REVERT: M 130 ASP cc_start: 0.8437 (OUTLIER) cc_final: 0.8237 (p0) REVERT: M 235 ASN cc_start: 0.7990 (OUTLIER) cc_final: 0.7735 (t0) REVERT: M 237 GLU cc_start: 0.8110 (mm-30) cc_final: 0.7590 (mm-30) REVERT: N 103 MET cc_start: 0.8627 (ttp) cc_final: 0.8362 (ttm) REVERT: N 111 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8494 (pp20) REVERT: N 112 ASP cc_start: 0.7930 (m-30) cc_final: 0.7705 (m-30) REVERT: O 198 LYS cc_start: -0.2064 (OUTLIER) cc_final: -0.2632 (ptmt) REVERT: O 225 MET cc_start: -0.2344 (ptm) cc_final: -0.2688 (tmm) outliers start: 38 outliers final: 16 residues processed: 216 average time/residue: 1.5640 time to fit residues: 367.0297 Evaluate side-chains 220 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 192 time to evaluate : 1.393 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 71 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 91 GLU 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 G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS 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 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 107 SER 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 2.9990 chunk 132 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 86 optimal weight: 60.0000 chunk 36 optimal weight: 6.9990 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 0.4980 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 77 optimal weight: 5.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 27 GLN C 38 ASN C 73 ASN D 60 ASN G 104 GLN H 60 ASN N 28 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16958 Z= 0.221 Angle : 0.561 9.012 24101 Z= 0.321 Chirality : 0.035 0.175 2706 Planarity : 0.004 0.047 2058 Dihedral : 28.443 165.479 4560 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 3.97 % Allowed : 24.93 % Favored : 71.09 % 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: 1.65 (0.24), residues: 1275 helix: 2.50 (0.21), residues: 577 sheet: 0.54 (0.35), residues: 230 loop : -0.41 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.003 0.001 HIS N 249 PHE 0.010 0.001 PHE A 67 TYR 0.014 0.001 TYR E 54 ARG 0.009 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 240 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 196 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8639 (OUTLIER) cc_final: 0.8385 (tttp) REVERT: B 92 ARG cc_start: 0.8713 (OUTLIER) cc_final: 0.8152 (ttp80) REVERT: C 71 ARG cc_start: 0.8100 (OUTLIER) cc_final: 0.7899 (ttp80) REVERT: C 91 GLU cc_start: 0.8582 (OUTLIER) cc_final: 0.7946 (tt0) REVERT: D 44 GLN cc_start: 0.8058 (tt0) cc_final: 0.7707 (mt0) REVERT: D 64 ASN cc_start: 0.8797 (m-40) cc_final: 0.8582 (m-40) REVERT: E 115 LYS cc_start: 0.8694 (mttt) cc_final: 0.8462 (mttp) REVERT: G 51 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7705 (tpt) REVERT: G 95 LYS cc_start: 0.8848 (OUTLIER) cc_final: 0.8348 (ttpt) REVERT: H 34 TYR cc_start: 0.9063 (m-80) cc_final: 0.8668 (m-80) REVERT: H 68 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.7361 (tp30) REVERT: H 90 GLU cc_start: 0.8754 (OUTLIER) cc_final: 0.7320 (mp0) REVERT: H 113 LYS cc_start: 0.8845 (ttpt) cc_final: 0.8496 (ttpt) REVERT: M 235 ASN cc_start: 0.7818 (OUTLIER) cc_final: 0.7484 (t0) REVERT: M 237 GLU cc_start: 0.8140 (mm-30) cc_final: 0.7517 (mm-30) REVERT: N 32 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7671 (mt-10) REVERT: N 103 MET cc_start: 0.8707 (ttp) cc_final: 0.8423 (ttm) REVERT: N 109 THR cc_start: 0.8277 (m) cc_final: 0.8067 (t) REVERT: N 111 GLU cc_start: 0.8813 (pp20) cc_final: 0.8530 (pp20) REVERT: O 198 LYS cc_start: -0.2004 (OUTLIER) cc_final: -0.2561 (ptmt) outliers start: 44 outliers final: 20 residues processed: 222 average time/residue: 1.6997 time to fit residues: 408.2047 Evaluate side-chains 226 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 196 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 71 ARG 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 E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS 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 H residue 109 SER Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 107 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 Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 107 optimal weight: 0.8980 chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 6.9990 chunk 146 optimal weight: 50.0000 chunk 91 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN E 108 ASN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16958 Z= 0.222 Angle : 0.564 8.866 24101 Z= 0.322 Chirality : 0.035 0.172 2706 Planarity : 0.004 0.046 2058 Dihedral : 28.381 165.264 4560 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.34 % Allowed : 25.56 % Favored : 71.09 % 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: 2.50 (0.21), residues: 578 sheet: 0.52 (0.35), residues: 230 loop : -0.47 (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 F 75 PHE 0.010 0.001 PHE A 67 TYR 0.016 0.001 TYR E 54 ARG 0.012 0.000 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 237 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 200 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.8627 (OUTLIER) cc_final: 0.8382 (tttp) REVERT: B 92 ARG cc_start: 0.8710 (OUTLIER) cc_final: 0.8165 (ttp80) REVERT: C 71 ARG cc_start: 0.8035 (OUTLIER) cc_final: 0.7833 (ttp80) REVERT: C 91 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.7922 (tt0) REVERT: D 32 GLU cc_start: 0.8383 (tt0) cc_final: 0.8019 (tt0) REVERT: D 44 GLN cc_start: 0.8042 (tt0) cc_final: 0.7688 (mt0) REVERT: D 64 ASN cc_start: 0.8811 (m-40) cc_final: 0.8595 (m-40) REVERT: E 115 LYS cc_start: 0.8711 (mttt) cc_final: 0.8484 (mttp) REVERT: G 51 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7696 (tpt) REVERT: G 95 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8375 (ttpt) REVERT: H 34 TYR cc_start: 0.9024 (m-80) cc_final: 0.8663 (m-80) REVERT: H 68 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7336 (tp30) REVERT: H 90 GLU cc_start: 0.8751 (OUTLIER) cc_final: 0.7329 (mp0) REVERT: H 113 LYS cc_start: 0.8843 (ttpt) cc_final: 0.8493 (ttpt) REVERT: M 175 GLU cc_start: 0.7436 (pt0) cc_final: 0.7123 (pm20) REVERT: M 235 ASN cc_start: 0.7816 (OUTLIER) cc_final: 0.7587 (t0) REVERT: M 237 GLU cc_start: 0.8166 (mm-30) cc_final: 0.7698 (mm-30) REVERT: N 32 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7671 (mt-10) REVERT: N 42 MET cc_start: 0.8968 (ptp) cc_final: 0.8743 (mpp) REVERT: N 57 GLN cc_start: 0.9052 (OUTLIER) cc_final: 0.7270 (mm110) REVERT: N 103 MET cc_start: 0.8602 (ttp) cc_final: 0.8351 (ttm) REVERT: N 111 GLU cc_start: 0.8824 (pp20) cc_final: 0.8560 (pp20) REVERT: N 112 ASP cc_start: 0.8065 (m-30) cc_final: 0.7823 (m-30) REVERT: N 169 MET cc_start: 0.8349 (ptp) cc_final: 0.8051 (mtp) outliers start: 37 outliers final: 20 residues processed: 219 average time/residue: 1.6352 time to fit residues: 387.6689 Evaluate side-chains 225 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 195 time to evaluate : 1.522 ------------------------------------------------------------------------------- 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 59 LYS Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 71 ARG 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 E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS 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 H residue 109 SER Chi-restraints excluded: chain M residue 32 GLU Chi-restraints excluded: chain M residue 33 LEU Chi-restraints excluded: chain M residue 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 138 VAL Chi-restraints excluded: chain M residue 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 216 VAL Chi-restraints excluded: chain N residue 239 ASP Chi-restraints excluded: chain O residue 174 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 20.0000 chunk 44 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 4.9990 chunk 99 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 115 optimal weight: 0.6980 chunk 133 optimal weight: 2.9990 chunk 140 optimal weight: 3.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 73 ASN C 104 GLN G 104 GLN H 46 HIS ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.3623 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= 0.289 Angle : 0.593 8.901 24101 Z= 0.336 Chirality : 0.037 0.168 2706 Planarity : 0.004 0.047 2058 Dihedral : 28.633 163.432 4560 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.61 % Allowed : 25.56 % Favored : 70.82 % 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: 1.44 (0.24), residues: 1275 helix: 2.34 (0.21), residues: 577 sheet: 0.47 (0.35), residues: 230 loop : -0.54 (0.28), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.003 0.001 HIS H 46 PHE 0.010 0.002 PHE A 67 TYR 0.018 0.002 TYR E 54 ARG 0.013 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 240 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 200 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 75 LYS cc_start: 0.8238 (mmtp) cc_final: 0.7845 (mmtt) REVERT: C 91 GLU cc_start: 0.8600 (tt0) cc_final: 0.7958 (tt0) REVERT: D 32 GLU cc_start: 0.8199 (tt0) cc_final: 0.7864 (tt0) REVERT: D 39 TYR cc_start: 0.7931 (t80) cc_final: 0.7588 (t80) REVERT: D 44 GLN cc_start: 0.8115 (tt0) cc_final: 0.7747 (mt0) REVERT: D 64 ASN cc_start: 0.8814 (m-40) cc_final: 0.8592 (m-40) REVERT: E 115 LYS cc_start: 0.8732 (mttt) cc_final: 0.8498 (mttp) REVERT: G 51 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.7675 (tpt) REVERT: G 95 LYS cc_start: 0.8864 (OUTLIER) cc_final: 0.8368 (ttpt) REVERT: H 34 TYR cc_start: 0.9079 (m-80) cc_final: 0.8743 (m-80) REVERT: H 68 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7387 (tp30) REVERT: H 90 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.7432 (mp0) REVERT: H 113 LYS cc_start: 0.8849 (ttpt) cc_final: 0.8483 (ttpt) REVERT: M 81 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8004 (ttpt) REVERT: M 235 ASN cc_start: 0.7875 (OUTLIER) cc_final: 0.7400 (t0) REVERT: M 237 GLU cc_start: 0.8213 (mm-30) cc_final: 0.7569 (mm-30) REVERT: N 32 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7719 (mt-10) REVERT: N 42 MET cc_start: 0.8937 (ptp) cc_final: 0.8617 (mpp) REVERT: N 57 GLN cc_start: 0.9061 (OUTLIER) cc_final: 0.7208 (mm110) REVERT: N 103 MET cc_start: 0.8710 (ttp) cc_final: 0.8486 (ttm) REVERT: N 111 GLU cc_start: 0.8829 (pp20) cc_final: 0.8527 (pp20) REVERT: O 198 LYS cc_start: -0.2279 (OUTLIER) cc_final: -0.2807 (ptmt) outliers start: 40 outliers final: 22 residues processed: 223 average time/residue: 1.6593 time to fit residues: 400.0243 Evaluate side-chains 229 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 199 time to evaluate : 1.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 129 ARG Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 51 MET Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 95 LYS 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 59 VAL Chi-restraints excluded: chain M residue 62 THR Chi-restraints excluded: chain M residue 81 LYS Chi-restraints excluded: chain M residue 100 THR 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 55 THR Chi-restraints excluded: chain N residue 57 GLN Chi-restraints excluded: chain N residue 93 THR 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 140 optimal weight: 4.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 123 optimal weight: 0.0070 chunk 129 optimal weight: 0.9990 chunk 89 optimal weight: 6.9990 chunk 144 optimal weight: 30.0000 overall best weight: 0.6602 ------------------------------------------------------------------------------- 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 60 ASN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.3733 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= 0.170 Angle : 0.553 9.082 24101 Z= 0.316 Chirality : 0.034 0.167 2706 Planarity : 0.004 0.041 2058 Dihedral : 28.275 163.968 4560 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.62 % Allowed : 26.83 % Favored : 70.55 % 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: 1.70 (0.24), residues: 1275 helix: 2.61 (0.21), residues: 577 sheet: 0.52 (0.35), residues: 230 loop : -0.45 (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 M 249 PHE 0.011 0.001 PHE A 67 TYR 0.013 0.001 TYR E 54 ARG 0.013 0.000 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 224 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 195 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 91 GLU cc_start: 0.8568 (tt0) cc_final: 0.7931 (tt0) REVERT: D 44 GLN cc_start: 0.8034 (tt0) cc_final: 0.7696 (mt0) REVERT: E 115 LYS cc_start: 0.8692 (mttt) cc_final: 0.8492 (mttp) REVERT: G 51 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7695 (tpt) REVERT: H 34 TYR cc_start: 0.8996 (m-80) cc_final: 0.8615 (m-80) REVERT: H 68 GLU cc_start: 0.7621 (OUTLIER) cc_final: 0.7341 (tp30) REVERT: H 90 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.7289 (mp0) REVERT: H 113 LYS cc_start: 0.8874 (ttpt) cc_final: 0.8509 (ttpt) REVERT: M 81 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.7957 (ttpt) REVERT: M 235 ASN cc_start: 0.7761 (OUTLIER) cc_final: 0.7525 (t0) REVERT: M 237 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7746 (mm-30) REVERT: N 32 GLU cc_start: 0.8145 (mm-30) cc_final: 0.7693 (mt-10) REVERT: N 42 MET cc_start: 0.8850 (ptp) cc_final: 0.8594 (mpp) REVERT: N 103 MET cc_start: 0.8551 (ttp) cc_final: 0.8334 (ttm) REVERT: N 111 GLU cc_start: 0.8788 (pp20) cc_final: 0.8588 (pp20) REVERT: N 169 MET cc_start: 0.8231 (ptp) cc_final: 0.7945 (ptm) REVERT: N 219 ARG cc_start: 0.8574 (mtm110) cc_final: 0.8257 (mtm110) REVERT: O 198 LYS cc_start: -0.2108 (OUTLIER) cc_final: -0.2641 (ptmt) outliers start: 29 outliers final: 18 residues processed: 217 average time/residue: 1.7028 time to fit residues: 399.8427 Evaluate side-chains 212 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 188 time to evaluate : 1.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain E residue 87 SER 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 81 LYS Chi-restraints excluded: chain M residue 100 THR 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 55 THR Chi-restraints excluded: chain N residue 109 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 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: 0.0980 chunk 100 optimal weight: 0.6980 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 0.0020 chunk 120 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 93 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 95 optimal weight: 5.9990 chunk 128 optimal weight: 5.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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 G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 16958 Z= 0.210 Angle : 0.567 9.253 24101 Z= 0.323 Chirality : 0.035 0.166 2706 Planarity : 0.004 0.047 2058 Dihedral : 28.387 162.905 4560 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 2.89 % Allowed : 26.02 % Favored : 71.09 % 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: 2.56 (0.21), residues: 578 sheet: 0.44 (0.34), residues: 232 loop : -0.46 (0.28), residues: 465 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 0.010 0.001 PHE A 67 TYR 0.018 0.001 TYR E 54 ARG 0.015 0.000 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 226 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 194 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 LYS cc_start: 0.8838 (tptp) cc_final: 0.8637 (tmtt) REVERT: C 71 ARG cc_start: 0.8057 (ttp80) cc_final: 0.7730 (ttp80) REVERT: C 91 GLU cc_start: 0.8578 (tt0) cc_final: 0.7956 (tt0) REVERT: D 32 GLU cc_start: 0.8231 (tt0) cc_final: 0.7848 (tt0) REVERT: D 39 TYR cc_start: 0.7939 (t80) cc_final: 0.7580 (t80) REVERT: D 44 GLN cc_start: 0.8070 (tt0) cc_final: 0.7735 (mt0) REVERT: E 115 LYS cc_start: 0.8713 (mttt) cc_final: 0.8476 (mttp) REVERT: G 51 MET cc_start: 0.8381 (OUTLIER) cc_final: 0.7694 (tpt) REVERT: G 59 THR cc_start: 0.9241 (t) cc_final: 0.8901 (m) REVERT: H 34 TYR cc_start: 0.9018 (m-80) cc_final: 0.8648 (m-80) REVERT: H 68 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.7338 (tp30) REVERT: H 90 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.7339 (mp0) REVERT: H 113 LYS cc_start: 0.8868 (ttpt) cc_final: 0.8491 (ttpt) REVERT: M 81 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.7969 (ttpt) REVERT: M 104 GLU cc_start: 0.8316 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: M 235 ASN cc_start: 0.7742 (OUTLIER) cc_final: 0.7288 (t0) REVERT: M 237 GLU cc_start: 0.8200 (mm-30) cc_final: 0.7589 (mm-30) REVERT: N 32 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7700 (mt-10) REVERT: N 169 MET cc_start: 0.8237 (ptp) cc_final: 0.7962 (ptm) REVERT: N 219 ARG cc_start: 0.8539 (mtm110) cc_final: 0.8138 (mtm110) REVERT: O 198 LYS cc_start: -0.2116 (OUTLIER) cc_final: -0.2649 (ptmt) outliers start: 32 outliers final: 20 residues processed: 213 average time/residue: 1.6529 time to fit residues: 380.9572 Evaluate side-chains 222 residues out of total 1110 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 195 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 87 SER 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 81 LYS Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 104 GLU 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 219 ARG Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 55 THR Chi-restraints excluded: chain N residue 109 THR 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 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: 0.0370 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.6980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 124 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 22 optimal weight: 1.9990 chunk 106 optimal weight: 0.1980 chunk 6 optimal weight: 3.9990 overall best weight: 0.7460 ------------------------------------------------------------------------------- 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 60 ASN G 104 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4039 r_free = 0.4039 target = 0.168639 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.103440 restraints weight = 20606.350| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.05 r_work: 0.2991 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 16958 Z= 0.184 Angle : 0.568 9.102 24101 Z= 0.323 Chirality : 0.035 0.166 2706 Planarity : 0.004 0.048 2058 Dihedral : 28.385 162.964 4560 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.07 % Allowed : 26.20 % Favored : 70.73 % 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: 1.67 (0.24), residues: 1275 helix: 2.58 (0.21), residues: 577 sheet: 0.43 (0.34), residues: 232 loop : -0.43 (0.28), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.011 0.001 PHE A 67 TYR 0.017 0.001 TYR E 54 ARG 0.016 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6504.48 seconds wall clock time: 115 minutes 54.99 seconds (6954.99 seconds total)