Starting phenix.real_space_refine on Fri Feb 16 18:32:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8evi_28630/02_2024/8evi_28630.pdb" } resolution = 2.64 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= 0.004 sd= 0.120 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 285 5.49 5 S 37 5.16 5 C 9296 2.51 5 N 2927 2.21 5 O 3612 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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 16157 Number of models: 1 Model: "" Number of chains: 13 Chain: "J" Number of atoms: 2931 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2931 Classifications: {'DNA': 143} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 142} Chain: "I" Number of atoms: 2929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 143, 2929 Classifications: {'DNA': 143} Link IDs: {'rna3p': 142} Chain breaks: 1 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: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 819 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: "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: 748 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 748 Classifications: {'peptide': 89} Link IDs: {'TRANS': 88} Time building chain proxies: 8.53, per 1000 atoms: 0.53 Number of scatterers: 16157 At special positions: 0 Unit cell: (140.448, 130.944, 141.504, 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 37 16.00 P 285 15.00 O 3612 8.00 N 2927 7.00 C 9296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 76 " - pdb=" SG CYS O 220 " distance=2.03 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: 7.45 Conformation dependent library (CDL) restraints added in 1.8 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: 2422 Finding SS restraints... Secondary structure from input PDB file: 45 helices and 24 sheets defined 47.6% alpha, 19.2% beta 138 base pairs and 264 stacking pairs defined. Time for finding SS restraints: 6.87 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.035A 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: 3.748A 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: 4.513A 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: 3.518A 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: 4.422A 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: 3.658A pdb=" N ARG O 235 " --> pdb=" O ALA O 231 " (cutoff:3.500A) removed outlier: 4.158A 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: 7.182A 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: 3.608A 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: 5.137A 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: 3.608A 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: 6.515A 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: 6.515A pdb=" N MET M 169 " --> pdb=" O GLU M 263 " (cutoff:3.500A) removed outlier: 3.606A 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: 4.497A 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: 7.253A 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: 6.307A 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: 4.831A pdb=" N TYR N 207 " --> pdb=" O LEU N 191 " (cutoff:3.500A) removed outlier: 6.819A 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: 4.150A 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: 3.887A 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: 342 hydrogen bonds 684 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 264 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 7.94 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: 1917 1.30 - 1.43: 5964 1.43 - 1.56: 8539 1.56 - 1.69: 568 1.69 - 1.82: 60 Bond restraints: 17048 Sorted by residual: bond pdb=" C HIS D 46 " pdb=" O HIS D 46 " ideal model delta sigma weight residual 1.238 1.174 0.064 1.08e-02 8.57e+03 3.53e+01 bond pdb=" C GLN E 125 " pdb=" O GLN E 125 " ideal model delta sigma weight residual 1.237 1.169 0.068 1.19e-02 7.06e+03 3.26e+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 2.69e+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 2.14e+01 bond pdb=" C ARG B 92 " pdb=" N GLN B 93 " ideal model delta sigma weight residual 1.334 1.275 0.058 1.30e-02 5.92e+03 2.00e+01 ... (remaining 17043 not shown) Histogram of bond angle deviations from ideal: 73.58 - 85.67: 1 85.67 - 97.76: 0 97.76 - 109.85: 5099 109.85 - 121.95: 15502 121.95 - 134.04: 3638 Bond angle restraints: 24240 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 73.58 36.22 1.23e+00 6.61e-01 8.67e+02 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 6.37e+01 angle pdb=" N LEU O 250 " pdb=" CA LEU O 250 " pdb=" CB LEU O 250 " ideal model delta sigma weight residual 112.13 120.06 -7.93 1.51e+00 4.39e-01 2.75e+01 angle pdb=" C4' DT I 149 " pdb=" C3' DT I 149 " pdb=" O3' DT I 149 " ideal model delta sigma weight residual 110.00 103.15 6.85 1.50e+00 4.44e-01 2.09e+01 angle pdb=" O3' DG I 148 " pdb=" C3' DG I 148 " pdb=" C2' DG I 148 " ideal model delta sigma weight residual 111.50 117.57 -6.07 1.50e+00 4.44e-01 1.64e+01 ... (remaining 24235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.16: 7847 33.16 - 66.32: 1678 66.32 - 99.48: 38 99.48 - 132.64: 0 132.64 - 165.81: 2 Dihedral angle restraints: 9565 sinusoidal: 5787 harmonic: 3778 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 -80.24 -42.36 0 2.50e+00 1.60e-01 2.87e+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 122.80 151.21 -28.41 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 -148.65 26.05 0 2.50e+00 1.60e-01 1.09e+02 ... (remaining 9562 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.243: 2717 0.243 - 0.486: 3 0.486 - 0.730: 0 0.730 - 0.973: 0 0.973 - 1.216: 1 Chirality restraints: 2721 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 1.29 1.22 2.00e-01 2.50e+01 3.70e+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 3.77e+00 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.23e+00 ... (remaining 2718 not shown) Planarity restraints: 2062 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 147 " -0.033 2.00e-02 2.50e+03 1.65e-02 6.84e+00 pdb=" N1 DT I 147 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 147 " -0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 147 " 0.024 2.00e-02 2.50e+03 pdb=" N3 DT I 147 " -0.016 2.00e-02 2.50e+03 pdb=" C4 DT I 147 " -0.011 2.00e-02 2.50e+03 pdb=" O4 DT I 147 " -0.007 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 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 91 " -0.013 2.00e-02 2.50e+03 2.61e-02 6.81e+00 pdb=" C LYS B 91 " 0.045 2.00e-02 2.50e+03 pdb=" O LYS B 91 " -0.017 2.00e-02 2.50e+03 pdb=" N ARG B 92 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 24 " 0.009 2.00e-02 2.50e+03 1.87e-02 3.49e+00 pdb=" CG ASP B 24 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP B 24 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP B 24 " 0.011 2.00e-02 2.50e+03 ... (remaining 2059 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 180 2.62 - 3.19: 12967 3.19 - 3.76: 28525 3.76 - 4.33: 39717 4.33 - 4.90: 58056 Nonbonded interactions: 139445 Sorted by model distance: nonbonded pdb=" O LYS O 249 " pdb=" CB LYS O 249 " model vdw 2.045 2.752 nonbonded pdb=" N4 DC J 15 " pdb=" O6 DG I 148 " model vdw 2.132 2.520 nonbonded pdb=" OG1 THR O 240 " pdb=" OE1 GLU O 242 " model vdw 2.164 2.440 nonbonded pdb=" NH2 ARG N 120 " pdb=" OD2 ASP N 130 " model vdw 2.199 2.520 nonbonded pdb=" NE2 GLN C 104 " pdb=" OE2 GLU E 94 " model vdw 2.208 2.520 ... (remaining 139440 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' and (resid 12 through 75 or resid 77 through 118)) selection = (chain 'G' and (resid 12 through 75 or resid 77 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: 0.720 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: 3.790 Check model and map are aligned: 0.250 Set scattering table: 0.160 Process input model: 48.680 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7623 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 0.068 17048 Z= 0.298 Angle : 0.685 36.222 24240 Z= 0.419 Chirality : 0.046 1.216 2721 Planarity : 0.004 0.037 2062 Dihedral : 26.592 165.806 7128 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.09 % Allowed : 25.27 % Favored : 74.64 % 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: 2.21 (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 206 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 205 time to evaluate : 1.415 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8528 (mtt) cc_final: 0.8185 (mtt) REVERT: C 36 LYS cc_start: 0.8677 (mmmm) cc_final: 0.8405 (mtpp) REVERT: C 42 ARG cc_start: 0.7903 (mtp85) cc_final: 0.7613 (mtp85) REVERT: D 82 LYS cc_start: 0.8566 (mtmm) cc_final: 0.8255 (mtmm) REVERT: D 113 LYS cc_start: 0.7665 (ttmt) cc_final: 0.7311 (ttpt) REVERT: E 64 LYS cc_start: 0.8323 (mttm) cc_final: 0.8115 (mttm) REVERT: G 73 ASN cc_start: 0.8401 (t0) cc_final: 0.7776 (t0) REVERT: G 91 GLU cc_start: 0.7964 (tt0) cc_final: 0.7641 (tt0) REVERT: H 34 TYR cc_start: 0.8495 (m-80) cc_final: 0.8253 (m-80) REVERT: H 60 ASN cc_start: 0.7991 (t0) cc_final: 0.7773 (t0) REVERT: H 68 GLU cc_start: 0.7171 (mt-10) cc_final: 0.6942 (mt-10) REVERT: H 82 LYS cc_start: 0.8270 (mttp) cc_final: 0.8008 (mtmm) REVERT: H 83 ARG cc_start: 0.7614 (mmt90) cc_final: 0.7369 (mmt90) REVERT: M 261 LYS cc_start: 0.8517 (mtpp) cc_final: 0.7384 (tptt) REVERT: M 263 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7155 (mp0) REVERT: N 25 GLN cc_start: 0.7806 (mm-40) cc_final: 0.7496 (mm-40) REVERT: N 102 TYR cc_start: 0.8262 (m-80) cc_final: 0.7988 (m-80) REVERT: N 111 GLU cc_start: 0.8429 (pp20) cc_final: 0.8081 (pp20) REVERT: N 112 ASP cc_start: 0.8336 (m-30) cc_final: 0.7761 (m-30) REVERT: N 169 MET cc_start: 0.7898 (ptp) cc_final: 0.7598 (pmm) REVERT: N 180 THR cc_start: 0.8952 (m) cc_final: 0.8696 (p) REVERT: N 219 ARG cc_start: 0.8173 (mtm110) cc_final: 0.7532 (ptm160) REVERT: N 261 LYS cc_start: 0.8461 (mtpm) cc_final: 0.8253 (ttmt) REVERT: N 263 GLU cc_start: 0.7613 (mm-30) cc_final: 0.7288 (tm-30) REVERT: O 187 MET cc_start: 0.3326 (ttt) cc_final: 0.3030 (ttp) REVERT: O 225 MET cc_start: 0.4728 (ptm) cc_final: 0.3896 (ppp) outliers start: 1 outliers final: 0 residues processed: 206 average time/residue: 1.8074 time to fit residues: 401.0279 Evaluate side-chains 166 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 1.384 ------------------------------------------------------------------------------- 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: 0.8980 chunk 115 optimal weight: 5.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 119 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 0.4980 chunk 88 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 76 GLN E 125 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 64 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 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: 0.7604 moved from start: 0.1078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 17048 Z= 0.196 Angle : 0.578 10.516 24240 Z= 0.334 Chirality : 0.036 0.232 2721 Planarity : 0.004 0.036 2062 Dihedral : 28.587 165.724 4605 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 3.88 % Allowed : 24.01 % Favored : 72.11 % 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: 1.54 (0.24), residues: 1275 helix: 2.44 (0.22), residues: 575 sheet: 0.46 (0.35), residues: 226 loop : -0.46 (0.28), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP O 193 HIS 0.003 0.001 HIS M 249 PHE 0.018 0.001 PHE O 254 TYR 0.012 0.001 TYR N 72 ARG 0.006 0.000 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 206 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 163 time to evaluate : 1.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 36 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8452 (mmmt) REVERT: C 42 ARG cc_start: 0.7833 (mtp85) cc_final: 0.7559 (mtp85) REVERT: D 82 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.8113 (mttm) REVERT: D 113 LYS cc_start: 0.7634 (ttmt) cc_final: 0.7320 (ttpt) REVERT: G 73 ASN cc_start: 0.8149 (t0) cc_final: 0.7769 (t0) REVERT: G 91 GLU cc_start: 0.7930 (tt0) cc_final: 0.7666 (tt0) REVERT: H 34 TYR cc_start: 0.8562 (m-80) cc_final: 0.8282 (m-80) REVERT: M 261 LYS cc_start: 0.8610 (mtpp) cc_final: 0.7421 (tptt) REVERT: N 25 GLN cc_start: 0.7827 (mm-40) cc_final: 0.7508 (mm-40) REVERT: N 103 MET cc_start: 0.8242 (OUTLIER) cc_final: 0.8005 (ttp) REVERT: N 112 ASP cc_start: 0.8013 (m-30) cc_final: 0.7617 (m-30) REVERT: N 169 MET cc_start: 0.7823 (ptp) cc_final: 0.7489 (ptm) REVERT: N 261 LYS cc_start: 0.8637 (mtpm) cc_final: 0.8329 (ttmt) REVERT: O 225 MET cc_start: 0.5849 (ptm) cc_final: 0.4794 (ppp) outliers start: 43 outliers final: 13 residues processed: 189 average time/residue: 1.6200 time to fit residues: 331.6078 Evaluate side-chains 168 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 153 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 41 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 76 GLN Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 100 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 3.9990 chunk 42 optimal weight: 0.3980 chunk 114 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 138 optimal weight: 4.9990 chunk 149 optimal weight: 7.9990 chunk 123 optimal weight: 6.9990 chunk 137 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 5.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 E 76 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN M 57 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 134 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 164 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17048 Z= 0.245 Angle : 0.581 9.806 24240 Z= 0.337 Chirality : 0.037 0.202 2721 Planarity : 0.004 0.032 2062 Dihedral : 28.697 165.495 4605 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.88 % Allowed : 23.74 % Favored : 72.38 % 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: 1.47 (0.24), residues: 1275 helix: 2.33 (0.22), residues: 573 sheet: 0.53 (0.35), residues: 226 loop : -0.47 (0.28), residues: 476 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 0.015 0.001 PHE O 254 TYR 0.013 0.001 TYR N 72 ARG 0.005 0.000 ARG H 96 *********************** 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 195 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 152 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7773 (mt-10) cc_final: 0.7483 (mt-10) REVERT: C 36 LYS cc_start: 0.8699 (mmmm) cc_final: 0.8430 (mmmt) REVERT: C 42 ARG cc_start: 0.7824 (mtp85) cc_final: 0.7520 (mtp85) REVERT: D 82 LYS cc_start: 0.8346 (OUTLIER) cc_final: 0.7974 (mttm) REVERT: D 113 LYS cc_start: 0.7912 (ttmt) cc_final: 0.7519 (ttpt) REVERT: E 90 MET cc_start: 0.7659 (OUTLIER) cc_final: 0.7046 (mtp) REVERT: G 73 ASN cc_start: 0.8129 (t0) cc_final: 0.7726 (t0) REVERT: G 95 LYS cc_start: 0.8389 (tttp) cc_final: 0.8156 (ttmt) REVERT: H 34 TYR cc_start: 0.8612 (m-80) cc_final: 0.8304 (m-80) REVERT: M 111 GLU cc_start: 0.8346 (OUTLIER) cc_final: 0.8031 (pp20) REVERT: M 235 ASN cc_start: 0.7569 (OUTLIER) cc_final: 0.6927 (m110) REVERT: M 263 GLU cc_start: 0.7324 (mp0) cc_final: 0.7111 (mp0) REVERT: N 103 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7928 (ttp) REVERT: N 169 MET cc_start: 0.7811 (ptp) cc_final: 0.7579 (ptm) REVERT: N 261 LYS cc_start: 0.8588 (mtpm) cc_final: 0.8213 (ttpt) REVERT: O 211 LEU cc_start: 0.4470 (OUTLIER) cc_final: 0.4264 (tm) REVERT: O 225 MET cc_start: 0.6185 (ptm) cc_final: 0.4953 (ppp) outliers start: 43 outliers final: 15 residues processed: 179 average time/residue: 1.6470 time to fit residues: 319.3967 Evaluate side-chains 173 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 152 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 211 LEU Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 0.8980 chunk 103 optimal weight: 3.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 5.9990 chunk 146 optimal weight: 30.0000 chunk 72 optimal weight: 1.9990 chunk 131 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN M 57 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7636 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17048 Z= 0.239 Angle : 0.573 9.425 24240 Z= 0.333 Chirality : 0.037 0.198 2721 Planarity : 0.004 0.031 2062 Dihedral : 28.670 165.917 4605 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.69 % Allowed : 23.10 % Favored : 72.20 % 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: 1.45 (0.24), residues: 1275 helix: 2.29 (0.22), residues: 573 sheet: 0.56 (0.35), residues: 226 loop : -0.47 (0.29), residues: 476 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 0.012 0.001 PHE O 254 TYR 0.013 0.001 TYR N 72 ARG 0.006 0.000 ARG H 96 *********************** 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 208 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 156 time to evaluate : 1.406 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7490 (mt-10) REVERT: C 36 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8401 (mmmt) REVERT: C 42 ARG cc_start: 0.7803 (mtp85) cc_final: 0.7501 (mtp85) REVERT: D 113 LYS cc_start: 0.7905 (ttmt) cc_final: 0.7516 (ttpt) REVERT: E 40 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7255 (mmm160) REVERT: E 90 MET cc_start: 0.7639 (OUTLIER) cc_final: 0.6993 (mtp) REVERT: G 73 ASN cc_start: 0.8093 (t0) cc_final: 0.7665 (t0) REVERT: H 34 TYR cc_start: 0.8606 (m-80) cc_final: 0.8288 (m-80) REVERT: M 111 GLU cc_start: 0.8434 (OUTLIER) cc_final: 0.8153 (pp20) REVERT: M 235 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.6899 (m110) REVERT: N 25 GLN cc_start: 0.7858 (mm-40) cc_final: 0.7527 (mm-40) REVERT: N 103 MET cc_start: 0.8141 (OUTLIER) cc_final: 0.7791 (ttp) REVERT: N 169 MET cc_start: 0.7860 (ptp) cc_final: 0.7646 (ptm) REVERT: N 261 LYS cc_start: 0.8593 (mtpm) cc_final: 0.8218 (ttpt) REVERT: O 253 GLN cc_start: 0.5499 (OUTLIER) cc_final: 0.4215 (mp10) outliers start: 52 outliers final: 23 residues processed: 194 average time/residue: 1.6352 time to fit residues: 344.0000 Evaluate side-chains 181 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 57 GLN Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 80 THR Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 228 ASP Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG 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: 4.9990 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 5.9990 chunk 109 optimal weight: 5.9990 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 3.9990 chunk 101 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 75 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 37 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 17048 Z= 0.366 Angle : 0.625 9.044 24240 Z= 0.360 Chirality : 0.040 0.194 2721 Planarity : 0.004 0.034 2062 Dihedral : 28.836 165.463 4605 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.51 % Allowed : 24.19 % Favored : 71.30 % 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: 1.05 (0.24), residues: 1275 helix: 1.95 (0.22), residues: 571 sheet: 0.60 (0.37), residues: 196 loop : -0.71 (0.27), residues: 508 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 0.010 0.002 PHE F 100 TYR 0.014 0.002 TYR N 72 ARG 0.006 0.001 ARG H 96 *********************** 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 200 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 150 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7926 (mt-10) cc_final: 0.7683 (mt-10) REVERT: C 36 LYS cc_start: 0.8715 (mmmm) cc_final: 0.8410 (mmmt) REVERT: C 42 ARG cc_start: 0.7808 (mtp85) cc_final: 0.7386 (mtp85) REVERT: C 74 LYS cc_start: 0.8077 (OUTLIER) cc_final: 0.7370 (mtmt) REVERT: D 82 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7798 (mtmm) REVERT: D 113 LYS cc_start: 0.7925 (ttmt) cc_final: 0.7529 (ttpt) REVERT: E 40 ARG cc_start: 0.7600 (OUTLIER) cc_final: 0.7347 (mmm160) REVERT: E 90 MET cc_start: 0.7648 (OUTLIER) cc_final: 0.7032 (mtp) REVERT: F 92 ARG cc_start: 0.8211 (OUTLIER) cc_final: 0.7608 (ptm160) REVERT: G 73 ASN cc_start: 0.8137 (t0) cc_final: 0.7741 (t0) REVERT: G 84 GLN cc_start: 0.8407 (OUTLIER) cc_final: 0.7468 (tm-30) REVERT: G 95 LYS cc_start: 0.8349 (tttp) cc_final: 0.8112 (ttmt) REVERT: H 82 LYS cc_start: 0.8031 (mtmm) cc_final: 0.7730 (mtmm) REVERT: M 25 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7700 (tt0) REVERT: M 111 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8186 (pp20) REVERT: M 235 ASN cc_start: 0.7565 (OUTLIER) cc_final: 0.6926 (m110) REVERT: N 23 GLU cc_start: 0.5964 (OUTLIER) cc_final: 0.5285 (tp30) REVERT: N 103 MET cc_start: 0.8228 (OUTLIER) cc_final: 0.7900 (ttp) REVERT: N 261 LYS cc_start: 0.8610 (mtpm) cc_final: 0.8248 (ttpt) outliers start: 50 outliers final: 19 residues processed: 182 average time/residue: 1.7105 time to fit residues: 336.4835 Evaluate side-chains 180 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 150 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 25 GLN Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 107 SER Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.9980 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 36 optimal weight: 1.9990 chunk 147 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN M 57 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 195 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: 0.7650 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17048 Z= 0.196 Angle : 0.592 8.511 24240 Z= 0.345 Chirality : 0.037 0.196 2721 Planarity : 0.004 0.046 2062 Dihedral : 28.825 165.994 4605 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.70 % Allowed : 25.18 % Favored : 71.12 % 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: 1.19 (0.24), residues: 1275 helix: 2.12 (0.22), residues: 573 sheet: 0.39 (0.36), residues: 206 loop : -0.61 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP O 193 HIS 0.004 0.001 HIS M 249 PHE 0.014 0.001 PHE N 220 TYR 0.012 0.001 TYR D 37 ARG 0.010 0.000 ARG N 176 *********************** 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 192 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 151 time to evaluate : 1.505 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7805 (mt-10) cc_final: 0.7539 (mt-10) REVERT: C 36 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8435 (mmmt) REVERT: C 42 ARG cc_start: 0.7780 (mtp85) cc_final: 0.7395 (mtp85) REVERT: C 74 LYS cc_start: 0.8055 (OUTLIER) cc_final: 0.7350 (mtmt) REVERT: D 82 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7793 (mtmm) REVERT: D 113 LYS cc_start: 0.7885 (ttmt) cc_final: 0.7500 (ttpt) REVERT: E 40 ARG cc_start: 0.7586 (OUTLIER) cc_final: 0.7330 (mmm160) REVERT: E 90 MET cc_start: 0.7593 (OUTLIER) cc_final: 0.7061 (mtp) REVERT: G 73 ASN cc_start: 0.8108 (t0) cc_final: 0.7705 (t0) REVERT: H 82 LYS cc_start: 0.8023 (mtmm) cc_final: 0.7641 (mtmm) REVERT: M 111 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.8188 (pp20) REVERT: M 235 ASN cc_start: 0.7534 (OUTLIER) cc_final: 0.6897 (m110) REVERT: N 103 MET cc_start: 0.8112 (OUTLIER) cc_final: 0.7788 (ttp) REVERT: N 176 ARG cc_start: 0.7568 (ttm-80) cc_final: 0.7286 (ttm-80) REVERT: N 261 LYS cc_start: 0.8607 (mtpm) cc_final: 0.8158 (ttpt) outliers start: 41 outliers final: 20 residues processed: 176 average time/residue: 1.7059 time to fit residues: 324.5287 Evaluate side-chains 176 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 149 time to evaluate : 1.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 39 SER Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 3.9990 chunk 16 optimal weight: 5.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 123 optimal weight: 7.9990 chunk 82 optimal weight: 3.9990 chunk 146 optimal weight: 0.5980 chunk 91 optimal weight: 10.0000 chunk 89 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 0.7673 moved from start: 0.1779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 17048 Z= 0.315 Angle : 0.604 8.288 24240 Z= 0.351 Chirality : 0.039 0.194 2721 Planarity : 0.004 0.035 2062 Dihedral : 28.795 166.320 4605 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.79 % Allowed : 25.36 % Favored : 70.85 % 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: 1.06 (0.24), residues: 1275 helix: 1.99 (0.22), residues: 571 sheet: 0.40 (0.36), residues: 206 loop : -0.67 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.005 0.001 HIS M 249 PHE 0.011 0.002 PHE O 254 TYR 0.018 0.002 TYR D 34 ARG 0.007 0.001 ARG N 176 *********************** 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 188 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 146 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7874 (mt-10) cc_final: 0.7599 (mt-10) REVERT: C 36 LYS cc_start: 0.8704 (mmmm) cc_final: 0.8424 (mmmt) REVERT: C 42 ARG cc_start: 0.7730 (mtp85) cc_final: 0.7306 (mtp85) REVERT: C 74 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7369 (mtmt) REVERT: D 36 ILE cc_start: 0.8530 (OUTLIER) cc_final: 0.8253 (pt) REVERT: D 113 LYS cc_start: 0.7907 (ttmt) cc_final: 0.7510 (ttpt) REVERT: E 40 ARG cc_start: 0.7580 (OUTLIER) cc_final: 0.7325 (mmm160) REVERT: E 90 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: G 73 ASN cc_start: 0.8107 (t0) cc_final: 0.7705 (t0) REVERT: G 84 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.7446 (tm-30) REVERT: H 82 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7711 (mtmm) REVERT: M 111 GLU cc_start: 0.8328 (OUTLIER) cc_final: 0.8044 (pp20) REVERT: M 235 ASN cc_start: 0.7552 (OUTLIER) cc_final: 0.6919 (m110) REVERT: N 23 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5221 (tp30) REVERT: N 103 MET cc_start: 0.8134 (OUTLIER) cc_final: 0.7787 (ttp) REVERT: N 176 ARG cc_start: 0.7629 (ttm-80) cc_final: 0.7353 (ttm-80) REVERT: N 177 VAL cc_start: 0.8993 (p) cc_final: 0.8783 (m) REVERT: N 261 LYS cc_start: 0.8615 (mtpm) cc_final: 0.8258 (ttpt) REVERT: O 253 GLN cc_start: 0.5419 (OUTLIER) cc_final: 0.4258 (mp10) outliers start: 42 outliers final: 18 residues processed: 173 average time/residue: 1.7273 time to fit residues: 323.0408 Evaluate side-chains 173 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 145 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 23 GLU Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR 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: 0.9980 chunk 87 optimal weight: 0.8980 chunk 44 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 93 optimal weight: 0.7980 chunk 99 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 10.0000 chunk 140 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7647 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 17048 Z= 0.208 Angle : 0.582 7.974 24240 Z= 0.340 Chirality : 0.037 0.198 2721 Planarity : 0.004 0.033 2062 Dihedral : 28.757 167.292 4605 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.43 % Allowed : 25.63 % Favored : 70.94 % 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: 1.23 (0.24), residues: 1275 helix: 2.13 (0.22), residues: 575 sheet: 0.44 (0.36), residues: 206 loop : -0.58 (0.28), residues: 494 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 0.029 0.001 PHE O 254 TYR 0.014 0.001 TYR D 34 ARG 0.008 0.000 ARG N 176 *********************** 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 183 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 145 time to evaluate : 1.492 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7801 (mt-10) cc_final: 0.7540 (mt-10) REVERT: C 36 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8434 (mmmt) REVERT: C 42 ARG cc_start: 0.7762 (mtp85) cc_final: 0.7372 (mtp85) REVERT: C 74 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7344 (mtmt) REVERT: D 82 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7779 (mtmm) REVERT: D 113 LYS cc_start: 0.7893 (ttmt) cc_final: 0.7506 (ttpt) REVERT: E 40 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7293 (mmm160) REVERT: E 90 MET cc_start: 0.7618 (OUTLIER) cc_final: 0.7053 (mtp) REVERT: G 73 ASN cc_start: 0.8078 (t0) cc_final: 0.7671 (t0) REVERT: H 82 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7728 (mtmm) REVERT: M 111 GLU cc_start: 0.8320 (OUTLIER) cc_final: 0.8051 (pp20) REVERT: M 235 ASN cc_start: 0.7514 (OUTLIER) cc_final: 0.6888 (m110) REVERT: N 103 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7761 (ttp) REVERT: N 169 MET cc_start: 0.7636 (OUTLIER) cc_final: 0.7314 (ptp) REVERT: N 176 ARG cc_start: 0.7560 (ttm-80) cc_final: 0.7278 (ttm-80) REVERT: N 261 LYS cc_start: 0.8639 (mtpm) cc_final: 0.8264 (ttpt) outliers start: 38 outliers final: 22 residues processed: 168 average time/residue: 1.6679 time to fit residues: 303.5730 Evaluate side-chains 176 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 146 time to evaluate : 1.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 111 GLU Chi-restraints excluded: chain M residue 130 ASP 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 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 168 SER Chi-restraints excluded: chain N residue 169 MET Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.3980 chunk 136 optimal weight: 0.8980 chunk 140 optimal weight: 2.9990 chunk 82 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 chunk 123 optimal weight: 9.9990 chunk 129 optimal weight: 4.9990 chunk 89 optimal weight: 2.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.1812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 17048 Z= 0.247 Angle : 0.588 7.975 24240 Z= 0.342 Chirality : 0.037 0.197 2721 Planarity : 0.004 0.034 2062 Dihedral : 28.661 167.190 4605 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.25 % Allowed : 26.08 % Favored : 70.67 % 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: 1.25 (0.24), residues: 1275 helix: 2.12 (0.22), residues: 575 sheet: 0.47 (0.36), residues: 206 loop : -0.55 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.006 0.001 HIS M 249 PHE 0.011 0.001 PHE O 254 TYR 0.015 0.002 TYR B 88 ARG 0.007 0.000 ARG D 83 *********************** 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 182 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 146 time to evaluate : 1.344 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7770 (mt-10) cc_final: 0.7479 (mt-10) REVERT: C 36 LYS cc_start: 0.8684 (mmmm) cc_final: 0.8403 (mmmt) REVERT: C 42 ARG cc_start: 0.7695 (mtp85) cc_final: 0.7379 (mtp85) REVERT: C 74 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7332 (mtmt) REVERT: D 82 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.7778 (mtmm) REVERT: D 113 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7515 (ttpt) REVERT: E 40 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7287 (mmm160) REVERT: E 90 MET cc_start: 0.7645 (OUTLIER) cc_final: 0.7059 (mtp) REVERT: G 73 ASN cc_start: 0.8081 (t0) cc_final: 0.7669 (t0) REVERT: H 82 LYS cc_start: 0.8025 (mtmm) cc_final: 0.7709 (mtmm) REVERT: M 235 ASN cc_start: 0.7515 (OUTLIER) cc_final: 0.6888 (m110) REVERT: N 103 MET cc_start: 0.8107 (OUTLIER) cc_final: 0.7768 (ttp) REVERT: N 162 MET cc_start: 0.9011 (mmp) cc_final: 0.8674 (mmm) REVERT: N 176 ARG cc_start: 0.7564 (ttm-80) cc_final: 0.7215 (ttm-80) REVERT: N 219 ARG cc_start: 0.8278 (mtm110) cc_final: 0.8057 (mtm110) REVERT: N 261 LYS cc_start: 0.8657 (mtpm) cc_final: 0.8285 (ttpt) outliers start: 36 outliers final: 21 residues processed: 167 average time/residue: 1.7518 time to fit residues: 316.2536 Evaluate side-chains 171 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 144 time to evaluate : 1.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 0.9990 chunk 68 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 151 optimal weight: 6.9990 chunk 139 optimal weight: 0.0980 chunk 120 optimal weight: 7.9990 chunk 12 optimal weight: 7.9990 chunk 93 optimal weight: 1.9990 chunk 73 optimal weight: 4.9990 chunk 95 optimal weight: 3.9990 chunk 128 optimal weight: 0.9980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7640 moved from start: 0.1829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 17048 Z= 0.200 Angle : 0.589 7.939 24240 Z= 0.342 Chirality : 0.036 0.198 2721 Planarity : 0.004 0.033 2062 Dihedral : 28.658 167.286 4605 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.62 % Allowed : 26.81 % Favored : 70.58 % 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: 1.31 (0.24), residues: 1275 helix: 2.19 (0.22), residues: 575 sheet: 0.48 (0.36), residues: 206 loop : -0.54 (0.28), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP O 193 HIS 0.005 0.001 HIS M 249 PHE 0.011 0.001 PHE O 254 TYR 0.033 0.001 TYR B 88 ARG 0.007 0.000 ARG D 83 ********************** 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 172 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 143 time to evaluate : 1.286 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 74 GLU cc_start: 0.7760 (mt-10) cc_final: 0.7469 (mt-10) REVERT: C 36 LYS cc_start: 0.8678 (mmmm) cc_final: 0.8399 (mmmt) REVERT: C 42 ARG cc_start: 0.7684 (mtp85) cc_final: 0.7374 (mtp85) REVERT: C 74 LYS cc_start: 0.8040 (OUTLIER) cc_final: 0.7323 (mtmt) REVERT: D 82 LYS cc_start: 0.8349 (OUTLIER) cc_final: 0.7775 (mtmm) REVERT: D 113 LYS cc_start: 0.7891 (ttmt) cc_final: 0.7506 (ttpt) REVERT: E 40 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7280 (mmm160) REVERT: E 90 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7056 (mtp) REVERT: G 73 ASN cc_start: 0.8071 (t0) cc_final: 0.7660 (t0) REVERT: H 39 TYR cc_start: 0.7775 (t80) cc_final: 0.7100 (t80) REVERT: H 82 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7706 (mtmm) REVERT: M 235 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.6880 (m110) REVERT: N 103 MET cc_start: 0.8099 (OUTLIER) cc_final: 0.7761 (ttp) REVERT: N 162 MET cc_start: 0.9005 (mmp) cc_final: 0.8635 (mmm) REVERT: N 176 ARG cc_start: 0.7531 (ttm-80) cc_final: 0.7192 (ttm-80) REVERT: N 261 LYS cc_start: 0.8654 (mtpm) cc_final: 0.8281 (ttpt) outliers start: 29 outliers final: 22 residues processed: 160 average time/residue: 1.7024 time to fit residues: 294.4372 Evaluate side-chains 170 residues out of total 1111 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 82 LYS Chi-restraints excluded: chain E residue 40 ARG Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 90 MET Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain M residue 38 THR Chi-restraints excluded: chain M residue 130 ASP Chi-restraints excluded: chain M residue 214 ASP Chi-restraints excluded: chain M residue 235 ASN Chi-restraints excluded: chain N residue 103 MET Chi-restraints excluded: chain N residue 130 ASP Chi-restraints excluded: chain N residue 139 THR Chi-restraints excluded: chain N residue 180 THR Chi-restraints excluded: chain N residue 187 ILE Chi-restraints excluded: chain N residue 191 LEU Chi-restraints excluded: chain N residue 192 SER Chi-restraints excluded: chain N residue 255 THR Chi-restraints excluded: chain O residue 226 THR Chi-restraints excluded: chain O residue 232 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 1.9990 chunk 111 optimal weight: 9.9990 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN D 60 ASN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN H 60 ASN M 27 GLN ** N 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 61 GLN ** O 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.157816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.106326 restraints weight = 16555.729| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 1.55 r_work: 0.3131 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 17048 Z= 0.324 Angle : 0.617 7.972 24240 Z= 0.357 Chirality : 0.039 0.201 2721 Planarity : 0.004 0.034 2062 Dihedral : 28.778 166.325 4605 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 3.07 % Allowed : 26.17 % Favored : 70.76 % 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: 1.07 (0.24), residues: 1275 helix: 1.96 (0.22), residues: 571 sheet: 0.45 (0.36), residues: 206 loop : -0.65 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP O 193 HIS 0.007 0.001 HIS M 249 PHE 0.012 0.002 PHE O 254 TYR 0.017 0.002 TYR D 34 ARG 0.007 0.001 ARG D 83 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5933.99 seconds wall clock time: 106 minutes 5.06 seconds (6365.06 seconds total)