Starting phenix.real_space_refine on Sun Apr 5 12:56:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.cif Found real_map, /net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.18 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.map" model { file = "/net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9kpz_62492/04_2026/9kpz_62492.cif" } resolution = 3.18 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.023 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 7 5.49 5 S 41 5.16 5 C 6838 2.51 5 N 1725 2.21 5 O 1836 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 19 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10447 Number of models: 1 Model: "" Number of chains: 17 Chain: "A" Number of atoms: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1727 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 214} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 1752 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1752 Classifications: {'peptide': 223} Link IDs: {'PTRANS': 5, 'TRANS': 217} Chain: "C" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1708 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 213} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'HIS:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 9 Chain: "D" Number of atoms: 1708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1708 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 212} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 1738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1738 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 5, 'TRANS': 215} Chain: "F" Number of atoms: 179 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 179 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "G" Number of atoms: 191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 191 Classifications: {'peptide': 25} Link IDs: {'PTRANS': 2, 'TRANS': 22} Chain: "H" Number of atoms: 214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 214 Classifications: {'peptide': 28} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 27} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "I" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 237 Classifications: {'peptide': 30} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 29} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "J" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 200 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 30 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 2, 'ARG:plan': 1, 'PHE:plan': 2} Unresolved non-hydrogen planarities: 27 Chain: "K" Number of atoms: 230 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 230 Classifications: {'peptide': 31} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'TRANS': 30} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 18 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 14 Chain: "L" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 220 Classifications: {'peptide': 29} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'TRANS': 28} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'ARG:plan': 1, 'PHE:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "B" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Chain: "D" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'3PE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'3PE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 2 Time building chain proxies: 2.42, per 1000 atoms: 0.23 Number of scatterers: 10447 At special positions: 0 Unit cell: (84, 94.08, 113.4, 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 41 16.00 P 7 15.00 O 1836 8.00 N 1725 7.00 C 6838 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.70 Conformation dependent library (CDL) restraints added in 440.9 milliseconds 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2452 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 0 sheets defined 90.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.26 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 Processing helix chain 'A' and resid 14 through 58 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.529A pdb=" N LEU A 65 " --> pdb=" O GLU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 74 through 77 removed outlier: 5.687A pdb=" N THR A 77 " --> pdb=" O ASP A 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 74 through 77' Processing helix chain 'A' and resid 78 through 95 removed outlier: 3.655A pdb=" N GLY A 86 " --> pdb=" O ILE A 82 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ARG A 95 " --> pdb=" O VAL A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 124 removed outlier: 3.724A pdb=" N VAL A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 158 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 167 through 184 removed outlier: 4.150A pdb=" N ALA A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N THR A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 221 removed outlier: 3.676A pdb=" N ALA A 215 " --> pdb=" O GLU A 211 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE A 216 " --> pdb=" O GLU A 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 6 through 13 Processing helix chain 'B' and resid 14 through 57 removed outlier: 3.648A pdb=" N TRP B 57 " --> pdb=" O GLU B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 72 removed outlier: 3.728A pdb=" N LEU B 65 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LYS B 72 " --> pdb=" O GLU B 68 " (cutoff:3.500A) Processing helix chain 'B' and resid 78 through 97 Processing helix chain 'B' and resid 100 through 124 removed outlier: 3.611A pdb=" N VAL B 104 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 155 removed outlier: 3.995A pdb=" N LEU B 130 " --> pdb=" O HIS B 126 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY B 131 " --> pdb=" O ILE B 127 " (cutoff:3.500A) Proline residue: B 138 - end of helix removed outlier: 3.904A pdb=" N ILE B 154 " --> pdb=" O MET B 150 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA B 155 " --> pdb=" O HIS B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 224 Proline residue: B 187 - end of helix removed outlier: 3.755A pdb=" N ASN B 193 " --> pdb=" O VAL B 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 13 removed outlier: 4.020A pdb=" N LEU C 11 " --> pdb=" O LEU C 7 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 58 Processing helix chain 'C' and resid 61 through 73 removed outlier: 4.051A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 78 through 97 removed outlier: 3.704A pdb=" N ASN C 97 " --> pdb=" O LEU C 93 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 125 removed outlier: 3.597A pdb=" N THR C 125 " --> pdb=" O GLU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 159 removed outlier: 4.000A pdb=" N LEU C 130 " --> pdb=" O HIS C 126 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY C 131 " --> pdb=" O ILE C 127 " (cutoff:3.500A) Proline residue: C 138 - end of helix removed outlier: 4.139A pdb=" N VAL C 159 " --> pdb=" O ALA C 155 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 222 removed outlier: 3.618A pdb=" N ILE C 171 " --> pdb=" O VAL C 167 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA C 174 " --> pdb=" O GLY C 170 " (cutoff:3.500A) Proline residue: C 187 - end of helix removed outlier: 4.866A pdb=" N ASN C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N ARG C 194 " --> pdb=" O MET C 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 12 Processing helix chain 'D' and resid 15 through 57 removed outlier: 3.548A pdb=" N TRP D 57 " --> pdb=" O GLU D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 72 removed outlier: 3.593A pdb=" N LEU D 65 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LYS D 72 " --> pdb=" O GLU D 68 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 76 Processing helix chain 'D' and resid 78 through 97 removed outlier: 3.784A pdb=" N ALA D 96 " --> pdb=" O ARG D 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.655A pdb=" N GLY D 107 " --> pdb=" O ALA D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 157 Proline residue: D 138 - end of helix Processing helix chain 'D' and resid 167 through 221 Proline residue: D 187 - end of helix Processing helix chain 'E' and resid 5 through 13 removed outlier: 3.566A pdb=" N LEU E 9 " --> pdb=" O ASN E 5 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 57 removed outlier: 4.300A pdb=" N TRP E 57 " --> pdb=" O GLU E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 72 removed outlier: 3.529A pdb=" N LEU E 65 " --> pdb=" O GLU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 96 removed outlier: 3.608A pdb=" N GLN E 81 " --> pdb=" O THR E 77 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 124 removed outlier: 3.708A pdb=" N VAL E 104 " --> pdb=" O ALA E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 158 removed outlier: 3.956A pdb=" N LEU E 130 " --> pdb=" O HIS E 126 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLY E 131 " --> pdb=" O ILE E 127 " (cutoff:3.500A) Proline residue: E 138 - end of helix removed outlier: 3.500A pdb=" N ALA E 158 " --> pdb=" O ILE E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 167 through 221 removed outlier: 3.562A pdb=" N ALA E 174 " --> pdb=" O GLY E 170 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ILE E 176 " --> pdb=" O ALA E 172 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ALA E 177 " --> pdb=" O GLU E 173 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR E 178 " --> pdb=" O ALA E 174 " (cutoff:3.500A) Proline residue: E 187 - end of helix removed outlier: 3.750A pdb=" N ASN E 193 " --> pdb=" O VAL E 189 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 23 Processing helix chain 'F' and resid 24 through 35 removed outlier: 3.967A pdb=" N LEU F 30 " --> pdb=" O LEU F 26 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ILE F 31 " --> pdb=" O VAL F 27 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N PHE F 32 " --> pdb=" O LEU F 28 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N MET F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA F 34 " --> pdb=" O LEU F 30 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N THR F 35 " --> pdb=" O ILE F 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 33 removed outlier: 3.589A pdb=" N VAL G 24 " --> pdb=" O PRO G 20 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N VAL G 27 " --> pdb=" O ASP G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 34 through 36 No H-bonds generated for 'chain 'G' and resid 34 through 36' Processing helix chain 'H' and resid 9 through 35 Processing helix chain 'I' and resid 9 through 37 Processing helix chain 'J' and resid 9 through 36 Processing helix chain 'K' and resid 9 through 37 Processing helix chain 'L' and resid 9 through 36 removed outlier: 3.530A pdb=" N ASP L 36 " --> pdb=" O TRP L 32 " (cutoff:3.500A) 903 hydrogen bonds defined for protein. 2700 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.62 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1642 1.31 - 1.44: 2748 1.44 - 1.56: 6115 1.56 - 1.69: 41 1.69 - 1.82: 82 Bond restraints: 10628 Sorted by residual: bond pdb=" C29 3PE A 301 " pdb=" C2A 3PE A 301 " ideal model delta sigma weight residual 1.524 1.346 0.178 2.00e-02 2.50e+03 7.95e+01 bond pdb=" C29 3PE E 301 " pdb=" C2A 3PE E 301 " ideal model delta sigma weight residual 1.524 1.346 0.178 2.00e-02 2.50e+03 7.89e+01 bond pdb=" C29 3PE D 301 " pdb=" C2A 3PE D 301 " ideal model delta sigma weight residual 1.524 1.346 0.178 2.00e-02 2.50e+03 7.88e+01 bond pdb=" C29 3PE B 302 " pdb=" C2A 3PE B 302 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.82e+01 bond pdb=" C29 3PE D 302 " pdb=" C2A 3PE D 302 " ideal model delta sigma weight residual 1.524 1.347 0.177 2.00e-02 2.50e+03 7.82e+01 ... (remaining 10623 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.96: 14062 2.96 - 5.91: 184 5.91 - 8.87: 42 8.87 - 11.83: 6 11.83 - 14.79: 7 Bond angle restraints: 14301 Sorted by residual: angle pdb=" O12 3PE C 301 " pdb=" P 3PE C 301 " pdb=" O14 3PE C 301 " ideal model delta sigma weight residual 123.79 109.00 14.79 3.00e+00 1.11e-01 2.43e+01 angle pdb=" O12 3PE D 302 " pdb=" P 3PE D 302 " pdb=" O14 3PE D 302 " ideal model delta sigma weight residual 123.79 109.05 14.74 3.00e+00 1.11e-01 2.41e+01 angle pdb=" O12 3PE E 301 " pdb=" P 3PE E 301 " pdb=" O14 3PE E 301 " ideal model delta sigma weight residual 123.79 109.22 14.57 3.00e+00 1.11e-01 2.36e+01 angle pdb=" O12 3PE D 301 " pdb=" P 3PE D 301 " pdb=" O14 3PE D 301 " ideal model delta sigma weight residual 123.79 109.37 14.42 3.00e+00 1.11e-01 2.31e+01 angle pdb=" O12 3PE A 301 " pdb=" P 3PE A 301 " pdb=" O14 3PE A 301 " ideal model delta sigma weight residual 123.79 109.38 14.41 3.00e+00 1.11e-01 2.31e+01 ... (remaining 14296 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.07: 5582 21.07 - 42.14: 655 42.14 - 63.22: 189 63.22 - 84.29: 19 84.29 - 105.36: 8 Dihedral angle restraints: 6453 sinusoidal: 2692 harmonic: 3761 Sorted by residual: dihedral pdb=" CA LEU F 26 " pdb=" C LEU F 26 " pdb=" N VAL F 27 " pdb=" CA VAL F 27 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" O21 3PE B 301 " pdb=" C2 3PE B 301 " pdb=" C3 3PE B 301 " pdb=" O31 3PE B 301 " ideal model delta sinusoidal sigma weight residual 60.47 -44.89 105.36 1 3.00e+01 1.11e-03 1.35e+01 dihedral pdb=" O21 3PE D 301 " pdb=" C2 3PE D 301 " pdb=" C3 3PE D 301 " pdb=" O31 3PE D 301 " ideal model delta sinusoidal sigma weight residual 60.47 156.31 -95.84 1 3.00e+01 1.11e-03 1.18e+01 ... (remaining 6450 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1183 0.032 - 0.064: 305 0.064 - 0.096: 122 0.096 - 0.129: 32 0.129 - 0.161: 2 Chirality restraints: 1644 Sorted by residual: chirality pdb=" CA LEU A 11 " pdb=" N LEU A 11 " pdb=" C LEU A 11 " pdb=" CB LEU A 11 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.46e-01 chirality pdb=" CB ILE D 82 " pdb=" CA ILE D 82 " pdb=" CG1 ILE D 82 " pdb=" CG2 ILE D 82 " both_signs ideal model delta sigma weight residual False 2.64 2.79 -0.15 2.00e-01 2.50e+01 5.56e-01 chirality pdb=" CA GLU A 68 " pdb=" N GLU A 68 " pdb=" C GLU A 68 " pdb=" CB GLU A 68 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 1641 not shown) Planarity restraints: 1762 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL F 19 " 0.023 2.00e-02 2.50e+03 4.66e-02 2.17e+01 pdb=" C VAL F 19 " -0.081 2.00e-02 2.50e+03 pdb=" O VAL F 19 " 0.029 2.00e-02 2.50e+03 pdb=" N PRO F 20 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE D 176 " 0.010 2.00e-02 2.50e+03 2.03e-02 4.11e+00 pdb=" C ILE D 176 " -0.035 2.00e-02 2.50e+03 pdb=" O ILE D 176 " 0.013 2.00e-02 2.50e+03 pdb=" N ALA D 177 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 75 " -0.010 2.00e-02 2.50e+03 1.97e-02 3.87e+00 pdb=" C ASN C 75 " 0.034 2.00e-02 2.50e+03 pdb=" O ASN C 75 " -0.013 2.00e-02 2.50e+03 pdb=" N LEU C 76 " -0.011 2.00e-02 2.50e+03 ... (remaining 1759 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 1980 2.78 - 3.31: 10537 3.31 - 3.84: 17549 3.84 - 4.37: 17921 4.37 - 4.90: 33206 Nonbonded interactions: 81193 Sorted by model distance: nonbonded pdb=" OD1 ASN C 43 " pdb=" NH2 ARG C 198 " model vdw 2.244 3.120 nonbonded pdb=" OE1 GLN E 81 " pdb=" OG SER E 115 " model vdw 2.246 3.040 nonbonded pdb=" OG SER D 115 " pdb=" NH2 ARG D 118 " model vdw 2.269 3.120 nonbonded pdb=" OG1 THR A 145 " pdb=" OG1 THR A 178 " model vdw 2.280 3.040 nonbonded pdb=" OG SER C 109 " pdb=" NH1 ARG C 110 " model vdw 2.281 3.120 ... (remaining 81188 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or (resid 99 through 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 158 or (resid 159 through 162 and \ (name N or name CA or name C or name O or name CB )) or resid 163 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 301)) selection = (chain 'B' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or (resid 99 through 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 158 or (resid 159 through 162 and \ (name N or name CA or name C or name O or name CB )) or resid 163 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 222 or resid 302)) selection = (chain 'C' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 164 or (resid 165 and (name N or name CA or name C or name \ O or name CB )) or resid 166 through 301)) selection = (chain 'D' and (resid 5 through 98 or (resid 99 through 100 and (name N or name \ CA or name C or name O or name CB )) or resid 101 through 158 or (resid 159 thro \ ugh 162 and (name N or name CA or name C or name O or name CB )) or resid 163 th \ rough 301)) selection = (chain 'E' and ((resid 5 and (name N or name CA or name C or name O or name CB ) \ ) or resid 6 through 98 or (resid 99 through 100 and (name N or name CA or name \ C or name O or name CB )) or resid 101 through 158 or (resid 159 through 162 and \ (name N or name CA or name C or name O or name CB )) or resid 163 through 164 o \ r (resid 165 and (name N or name CA or name C or name O or name CB )) or resid 1 \ 66 through 301)) } ncs_group { reference = chain 'F' selection = (chain 'G' and resid 13 through 35) } ncs_group { reference = (chain 'H' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 34 or (re \ sid 35 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'I' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 34 or (re \ sid 35 and (name N or name CA or name C or name O or name CB )))) selection = (chain 'J' and (resid 8 through 10 or (resid 11 and (name N or name CA or name C \ or name O or name CB )) or resid 12 through 35)) selection = (chain 'K' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 through 12 or (resid 13 through 15 and (name N or name CA or name C \ or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (nam \ e N or name CA or name C or name O or name CB )) or resid 30 through 35)) selection = (chain 'L' and ((resid 8 and (name N or name CA or name C or name O or name CB ) \ ) or resid 9 or (resid 10 through 11 and (name N or name CA or name C or name O \ or name CB )) or resid 12 or (resid 13 through 15 and (name N or name CA or name \ C or name O or name CB )) or resid 16 through 26 or (resid 27 through 29 and (n \ ame N or name CA or name C or name O or name CB )) or resid 30 through 35)) } 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: 1.990 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: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.930 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 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:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.008 0.178 10628 Z= 0.421 Angle : 0.863 14.787 14301 Z= 0.385 Chirality : 0.036 0.161 1644 Planarity : 0.004 0.047 1762 Dihedral : 19.281 105.361 4001 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.16 % Allowed : 3.62 % Favored : 96.23 % Rotamer: Outliers : 0.38 % Allowed : 13.27 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.72 (0.24), residues: 1272 helix: 3.01 (0.15), residues: 1118 sheet: None (None), residues: 0 loop : -2.26 (0.48), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 64 TYR 0.021 0.001 TYR D 84 PHE 0.013 0.001 PHE C 52 TRP 0.021 0.001 TRP B 57 HIS 0.004 0.000 HIS A 218 Details of bonding type rmsd covalent geometry : bond 0.00833 (10628) covalent geometry : angle 0.86267 (14301) hydrogen bonds : bond 0.10074 ( 903) hydrogen bonds : angle 4.24086 ( 2700) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 175 time to evaluate : 0.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.7769 (mm-40) cc_final: 0.7093 (pt0) REVERT: B 57 TRP cc_start: 0.8093 (m100) cc_final: 0.7888 (m100) REVERT: B 72 LYS cc_start: 0.8471 (pttp) cc_final: 0.8262 (pptt) REVERT: B 214 THR cc_start: 0.8988 (t) cc_final: 0.8778 (t) REVERT: D 112 MET cc_start: 0.5921 (tmm) cc_final: 0.5715 (tmm) REVERT: D 113 ARG cc_start: 0.7839 (ttp80) cc_final: 0.7528 (ptm160) outliers start: 4 outliers final: 0 residues processed: 177 average time/residue: 0.1150 time to fit residues: 27.9993 Evaluate side-chains 169 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 169 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 108 optimal weight: 0.1980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 33 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS C 126 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.201476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.154050 restraints weight = 12126.223| |-----------------------------------------------------------------------------| r_work (start): 0.3903 rms_B_bonded: 2.37 r_work: 0.3695 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.0760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 10628 Z= 0.125 Angle : 0.520 6.789 14301 Z= 0.267 Chirality : 0.036 0.238 1644 Planarity : 0.003 0.038 1762 Dihedral : 14.738 105.029 1704 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.59 % Favored : 97.17 % Rotamer: Outliers : 1.83 % Allowed : 13.37 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.16 (0.23), residues: 1272 helix: 3.28 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -2.09 (0.49), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.012 0.001 TYR E 66 PHE 0.013 0.001 PHE C 52 TRP 0.008 0.001 TRP L 32 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00247 (10628) covalent geometry : angle 0.51952 (14301) hydrogen bonds : bond 0.04775 ( 903) hydrogen bonds : angle 3.23363 ( 2700) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 147 TRP cc_start: 0.7381 (t-100) cc_final: 0.7108 (t-100) REVERT: B 214 THR cc_start: 0.8951 (t) cc_final: 0.8739 (t) REVERT: D 64 ARG cc_start: 0.8352 (mmm160) cc_final: 0.8128 (mmm160) REVERT: D 112 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.5687 (tmm) REVERT: E 207 ASP cc_start: 0.8337 (t0) cc_final: 0.8097 (t0) outliers start: 19 outliers final: 11 residues processed: 191 average time/residue: 0.1098 time to fit residues: 28.8907 Evaluate side-chains 183 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 171 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 9.9990 chunk 63 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 81 optimal weight: 0.0980 chunk 7 optimal weight: 10.0000 chunk 2 optimal weight: 0.7980 chunk 114 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 82 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 HIS D 208 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.200201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150576 restraints weight = 12188.111| |-----------------------------------------------------------------------------| r_work (start): 0.3869 rms_B_bonded: 2.20 r_work: 0.3688 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10628 Z= 0.129 Angle : 0.509 5.997 14301 Z= 0.262 Chirality : 0.036 0.208 1644 Planarity : 0.003 0.035 1762 Dihedral : 13.802 100.568 1704 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.91 % Favored : 96.86 % Rotamer: Outliers : 2.21 % Allowed : 15.19 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.36 (0.23), residues: 1272 helix: 3.42 (0.15), residues: 1123 sheet: None (None), residues: 0 loop : -2.04 (0.48), residues: 149 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.011 0.001 TYR C 84 PHE 0.014 0.001 PHE C 52 TRP 0.010 0.001 TRP L 32 HIS 0.003 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00273 (10628) covalent geometry : angle 0.50869 (14301) hydrogen bonds : bond 0.04827 ( 903) hydrogen bonds : angle 3.12636 ( 2700) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 179 time to evaluate : 0.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 72 LYS cc_start: 0.8352 (pttp) cc_final: 0.7999 (pptt) REVERT: B 147 TRP cc_start: 0.7367 (t-100) cc_final: 0.7078 (t-100) REVERT: B 214 THR cc_start: 0.8873 (t) cc_final: 0.8568 (t) REVERT: C 72 LYS cc_start: 0.8021 (tttt) cc_final: 0.7791 (tttm) REVERT: D 64 ARG cc_start: 0.8410 (mmm160) cc_final: 0.8088 (mmm160) REVERT: D 113 ARG cc_start: 0.7792 (ttp80) cc_final: 0.7462 (ptm160) REVERT: D 166 MET cc_start: 0.5860 (OUTLIER) cc_final: 0.5204 (ptt) REVERT: E 207 ASP cc_start: 0.8358 (t0) cc_final: 0.8067 (t0) outliers start: 23 outliers final: 14 residues processed: 187 average time/residue: 0.1087 time to fit residues: 28.1543 Evaluate side-chains 186 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 26 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 24 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 95 optimal weight: 7.9990 chunk 104 optimal weight: 0.0070 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 6 optimal weight: 0.3980 chunk 94 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 overall best weight: 0.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS C 67 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.200182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.152281 restraints weight = 12272.367| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 2.38 r_work: 0.3671 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10628 Z= 0.122 Angle : 0.499 6.445 14301 Z= 0.257 Chirality : 0.035 0.218 1644 Planarity : 0.003 0.036 1762 Dihedral : 13.226 97.702 1704 Min Nonbonded Distance : 2.352 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.24 % Allowed : 2.75 % Favored : 97.01 % Rotamer: Outliers : 2.31 % Allowed : 15.96 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.42 (0.23), residues: 1272 helix: 3.45 (0.15), residues: 1124 sheet: None (None), residues: 0 loop : -1.99 (0.48), residues: 148 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 113 TYR 0.009 0.001 TYR C 139 PHE 0.010 0.001 PHE C 52 TRP 0.010 0.001 TRP L 32 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00250 (10628) covalent geometry : angle 0.49899 (14301) hydrogen bonds : bond 0.04709 ( 903) hydrogen bonds : angle 3.07149 ( 2700) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7655 (mm-30) REVERT: B 147 TRP cc_start: 0.7397 (t-100) cc_final: 0.7112 (t-100) REVERT: B 214 THR cc_start: 0.8944 (t) cc_final: 0.8646 (t) REVERT: C 156 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7359 (tt) REVERT: D 64 ARG cc_start: 0.8420 (mmm160) cc_final: 0.8059 (mmm160) REVERT: D 112 MET cc_start: 0.6467 (OUTLIER) cc_final: 0.6207 (tmm) REVERT: D 166 MET cc_start: 0.5758 (OUTLIER) cc_final: 0.5073 (ptt) REVERT: E 207 ASP cc_start: 0.8384 (t0) cc_final: 0.8126 (t0) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 0.0981 time to fit residues: 25.4067 Evaluate side-chains 184 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 166 time to evaluate : 0.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 156 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 166 MET Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 1.9990 chunk 81 optimal weight: 4.9990 chunk 29 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 97 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 79 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS C 67 GLN D 208 ASN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.197129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3813 r_free = 0.3813 target = 0.148656 restraints weight = 12351.107| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.58 r_work: 0.3633 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10628 Z= 0.151 Angle : 0.540 7.867 14301 Z= 0.278 Chirality : 0.037 0.207 1644 Planarity : 0.003 0.036 1762 Dihedral : 12.862 94.447 1704 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.38 % Favored : 96.54 % Rotamer: Outliers : 2.69 % Allowed : 17.02 % Favored : 80.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.24 (0.23), residues: 1272 helix: 3.33 (0.14), residues: 1126 sheet: None (None), residues: 0 loop : -2.13 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 113 TYR 0.013 0.001 TYR C 84 PHE 0.014 0.001 PHE E 209 TRP 0.011 0.001 TRP L 32 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00350 (10628) covalent geometry : angle 0.54041 (14301) hydrogen bonds : bond 0.05228 ( 903) hydrogen bonds : angle 3.14649 ( 2700) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 0.348 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7608 (mm-30) REVERT: B 147 TRP cc_start: 0.7392 (t-100) cc_final: 0.7077 (t-100) REVERT: B 214 THR cc_start: 0.8908 (OUTLIER) cc_final: 0.8628 (t) REVERT: C 67 GLN cc_start: 0.8010 (OUTLIER) cc_final: 0.7072 (mp10) REVERT: D 64 ARG cc_start: 0.8455 (mmm160) cc_final: 0.8057 (mmm160) REVERT: D 113 ARG cc_start: 0.7713 (ttp80) cc_final: 0.7393 (ttp80) REVERT: E 142 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8435 (mt) REVERT: E 207 ASP cc_start: 0.8394 (t0) cc_final: 0.8107 (t0) outliers start: 28 outliers final: 20 residues processed: 181 average time/residue: 0.1024 time to fit residues: 26.2884 Evaluate side-chains 191 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 167 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 67 GLN Chi-restraints excluded: chain C residue 149 ILE Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 77 THR Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 199 VAL Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 21 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 16 optimal weight: 0.6980 chunk 103 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 55 optimal weight: 0.9990 chunk 1 optimal weight: 0.5980 chunk 113 optimal weight: 6.9990 chunk 121 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.199131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.150939 restraints weight = 12314.278| |-----------------------------------------------------------------------------| r_work (start): 0.3865 rms_B_bonded: 2.40 r_work: 0.3657 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10628 Z= 0.126 Angle : 0.519 7.132 14301 Z= 0.267 Chirality : 0.035 0.195 1644 Planarity : 0.003 0.037 1762 Dihedral : 12.344 92.331 1704 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.91 % Favored : 97.01 % Rotamer: Outliers : 2.12 % Allowed : 18.17 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.33 (0.23), residues: 1272 helix: 3.39 (0.14), residues: 1126 sheet: None (None), residues: 0 loop : -2.09 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 113 TYR 0.010 0.001 TYR C 139 PHE 0.009 0.001 PHE E 209 TRP 0.013 0.001 TRP L 32 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00265 (10628) covalent geometry : angle 0.51907 (14301) hydrogen bonds : bond 0.04873 ( 903) hydrogen bonds : angle 3.09213 ( 2700) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 121 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7661 (mm-30) REVERT: B 147 TRP cc_start: 0.7422 (t-100) cc_final: 0.7045 (t-100) REVERT: B 214 THR cc_start: 0.8951 (OUTLIER) cc_final: 0.8659 (t) REVERT: D 64 ARG cc_start: 0.8460 (mmm160) cc_final: 0.8061 (mmm160) REVERT: D 112 MET cc_start: 0.6557 (OUTLIER) cc_final: 0.6321 (tmm) REVERT: E 142 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8476 (mt) REVERT: E 207 ASP cc_start: 0.8388 (t0) cc_final: 0.8098 (t0) outliers start: 22 outliers final: 14 residues processed: 186 average time/residue: 0.1128 time to fit residues: 29.0487 Evaluate side-chains 187 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 169 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 47 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 77 optimal weight: 0.0980 chunk 120 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 113 optimal weight: 5.9990 chunk 70 optimal weight: 4.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS D 208 ASN E 37 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.196645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.147344 restraints weight = 12215.342| |-----------------------------------------------------------------------------| r_work (start): 0.3780 rms_B_bonded: 2.15 r_work: 0.3589 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.1429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 10628 Z= 0.150 Angle : 0.551 7.335 14301 Z= 0.284 Chirality : 0.036 0.200 1644 Planarity : 0.003 0.037 1762 Dihedral : 12.093 88.848 1704 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.22 % Favored : 96.70 % Rotamer: Outliers : 2.40 % Allowed : 18.37 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.23), residues: 1272 helix: 3.32 (0.14), residues: 1126 sheet: None (None), residues: 0 loop : -2.10 (0.48), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 113 TYR 0.015 0.001 TYR C 84 PHE 0.014 0.001 PHE E 209 TRP 0.015 0.001 TRP L 32 HIS 0.004 0.001 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00345 (10628) covalent geometry : angle 0.55070 (14301) hydrogen bonds : bond 0.05292 ( 903) hydrogen bonds : angle 3.15728 ( 2700) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: B 121 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: B 147 TRP cc_start: 0.7465 (t-100) cc_final: 0.7108 (t-100) REVERT: B 214 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8701 (t) REVERT: D 64 ARG cc_start: 0.8476 (mmm160) cc_final: 0.8061 (mmm160) REVERT: D 113 ARG cc_start: 0.7766 (ttp80) cc_final: 0.7546 (ptm160) REVERT: E 142 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8436 (mt) REVERT: E 207 ASP cc_start: 0.8368 (t0) cc_final: 0.8096 (t0) outliers start: 25 outliers final: 19 residues processed: 181 average time/residue: 0.1052 time to fit residues: 26.7492 Evaluate side-chains 192 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain D residue 208 ASN Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 32 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 100 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS D 208 ASN E 37 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.197725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.148636 restraints weight = 12166.149| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 2.14 r_work: 0.3600 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.1464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10628 Z= 0.139 Angle : 0.553 8.581 14301 Z= 0.284 Chirality : 0.036 0.194 1644 Planarity : 0.003 0.037 1762 Dihedral : 11.743 84.764 1704 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 5.08 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.40 % Allowed : 18.46 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.30 (0.23), residues: 1272 helix: 3.34 (0.14), residues: 1130 sheet: None (None), residues: 0 loop : -2.02 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.011 0.001 TYR C 139 PHE 0.011 0.001 PHE E 209 TRP 0.016 0.001 TRP L 32 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00308 (10628) covalent geometry : angle 0.55268 (14301) hydrogen bonds : bond 0.05119 ( 903) hydrogen bonds : angle 3.12930 ( 2700) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8306 (pm20) REVERT: A 124 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7476 (tm-30) REVERT: B 37 GLN cc_start: 0.7759 (mm-40) cc_final: 0.6631 (pt0) REVERT: B 121 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: B 147 TRP cc_start: 0.7464 (t-100) cc_final: 0.7093 (t-100) REVERT: B 214 THR cc_start: 0.8994 (OUTLIER) cc_final: 0.8733 (t) REVERT: D 64 ARG cc_start: 0.8469 (mmm160) cc_final: 0.8049 (mmm160) REVERT: E 142 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8453 (mt) REVERT: E 207 ASP cc_start: 0.8371 (t0) cc_final: 0.8089 (t0) outliers start: 25 outliers final: 16 residues processed: 182 average time/residue: 0.1057 time to fit residues: 26.9281 Evaluate side-chains 190 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 170 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 18 optimal weight: 0.8980 chunk 89 optimal weight: 1.9990 chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 87 optimal weight: 0.0770 chunk 85 optimal weight: 1.9990 overall best weight: 1.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 HIS D 208 ASN E 37 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.196515 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.147313 restraints weight = 12166.778| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 2.14 r_work: 0.3595 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 10628 Z= 0.152 Angle : 0.585 14.594 14301 Z= 0.298 Chirality : 0.037 0.197 1644 Planarity : 0.003 0.037 1762 Dihedral : 11.407 79.235 1704 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.14 % Favored : 96.78 % Rotamer: Outliers : 2.50 % Allowed : 18.85 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.23), residues: 1272 helix: 3.30 (0.14), residues: 1130 sheet: None (None), residues: 0 loop : -2.05 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 113 TYR 0.017 0.002 TYR C 84 PHE 0.012 0.001 PHE E 209 TRP 0.018 0.001 TRP L 32 HIS 0.004 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00347 (10628) covalent geometry : angle 0.58525 (14301) hydrogen bonds : bond 0.05329 ( 903) hydrogen bonds : angle 3.17175 ( 2700) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 171 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLU cc_start: 0.8610 (OUTLIER) cc_final: 0.8300 (pm20) REVERT: A 124 GLU cc_start: 0.7798 (tm-30) cc_final: 0.7569 (tm-30) REVERT: B 37 GLN cc_start: 0.7792 (mm-40) cc_final: 0.6659 (pt0) REVERT: B 121 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7716 (mm-30) REVERT: B 147 TRP cc_start: 0.7488 (t-100) cc_final: 0.7127 (t-100) REVERT: B 214 THR cc_start: 0.9007 (OUTLIER) cc_final: 0.8748 (t) REVERT: C 222 PHE cc_start: 0.2632 (OUTLIER) cc_final: 0.2137 (t80) REVERT: D 64 ARG cc_start: 0.8479 (mmm160) cc_final: 0.8057 (mmm160) REVERT: D 113 ARG cc_start: 0.7763 (ttp80) cc_final: 0.7545 (ptm160) REVERT: D 220 GLN cc_start: 0.7701 (tm-30) cc_final: 0.7393 (tm-30) REVERT: E 72 LYS cc_start: 0.6817 (mtmm) cc_final: 0.6569 (mtmm) REVERT: E 142 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8441 (mt) REVERT: E 207 ASP cc_start: 0.8358 (t0) cc_final: 0.8057 (t0) outliers start: 26 outliers final: 19 residues processed: 181 average time/residue: 0.1068 time to fit residues: 27.3244 Evaluate side-chains 194 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 170 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLU Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 214 THR Chi-restraints excluded: chain B residue 216 ILE Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 190 MET Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain E residue 216 ILE Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 46 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 28 optimal weight: 6.9990 chunk 60 optimal weight: 0.0980 chunk 89 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 105 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 102 optimal weight: 0.1980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 GLN B 218 HIS D 208 ASN E 37 GLN ** E 117 ASN ** 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 = 0.4370 r_free = 0.4370 target = 0.199364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.150941 restraints weight = 12062.220| |-----------------------------------------------------------------------------| r_work (start): 0.3867 rms_B_bonded: 2.12 r_work: 0.3678 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10628 Z= 0.130 Angle : 0.571 15.503 14301 Z= 0.292 Chirality : 0.036 0.190 1644 Planarity : 0.003 0.038 1762 Dihedral : 10.953 75.097 1704 Min Nonbonded Distance : 2.337 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.99 % Favored : 96.93 % Rotamer: Outliers : 2.12 % Allowed : 19.23 % Favored : 78.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.40 (0.23), residues: 1272 helix: 3.43 (0.14), residues: 1126 sheet: None (None), residues: 0 loop : -2.06 (0.50), residues: 146 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 118 TYR 0.010 0.001 TYR E 66 PHE 0.008 0.001 PHE C 52 TRP 0.018 0.001 TRP L 32 HIS 0.003 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00270 (10628) covalent geometry : angle 0.57087 (14301) hydrogen bonds : bond 0.04836 ( 903) hydrogen bonds : angle 3.09859 ( 2700) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2544 Ramachandran restraints generated. 1272 Oldfield, 0 Emsley, 1272 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 37 GLN cc_start: 0.7679 (mm110) cc_final: 0.6598 (pt0) REVERT: B 48 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7935 (tm-30) REVERT: B 121 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7666 (mm-30) REVERT: B 147 TRP cc_start: 0.7453 (t-100) cc_final: 0.7080 (t-100) REVERT: B 214 THR cc_start: 0.8936 (t) cc_final: 0.8654 (t) REVERT: C 222 PHE cc_start: 0.2590 (OUTLIER) cc_final: 0.2079 (t80) REVERT: D 64 ARG cc_start: 0.8486 (mmm160) cc_final: 0.8070 (mmm160) REVERT: D 113 ARG cc_start: 0.7734 (ttp80) cc_final: 0.7528 (ptm160) REVERT: E 72 LYS cc_start: 0.6745 (mtmm) cc_final: 0.6500 (mtmm) REVERT: E 142 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8367 (mt) REVERT: E 207 ASP cc_start: 0.8328 (t0) cc_final: 0.7905 (t0) REVERT: E 211 GLU cc_start: 0.8755 (mm-30) cc_final: 0.8424 (mm-30) outliers start: 22 outliers final: 16 residues processed: 183 average time/residue: 0.1064 time to fit residues: 27.5074 Evaluate side-chains 187 residues out of total 1063 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 168 time to evaluate : 0.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 THR Chi-restraints excluded: chain A residue 121 GLU Chi-restraints excluded: chain B residue 121 GLU Chi-restraints excluded: chain B residue 166 MET Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain C residue 7 LEU Chi-restraints excluded: chain C residue 189 VAL Chi-restraints excluded: chain C residue 222 PHE Chi-restraints excluded: chain D residue 154 ILE Chi-restraints excluded: chain D residue 163 THR Chi-restraints excluded: chain E residue 50 GLU Chi-restraints excluded: chain E residue 77 THR Chi-restraints excluded: chain E residue 142 LEU Chi-restraints excluded: chain E residue 146 VAL Chi-restraints excluded: chain F residue 23 ASP Chi-restraints excluded: chain F residue 33 MET Chi-restraints excluded: chain G residue 30 LEU Chi-restraints excluded: chain H residue 12 LEU Chi-restraints excluded: chain H residue 16 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 38 optimal weight: 0.4980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 218 HIS E 37 GLN ** E 117 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.196629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.147493 restraints weight = 12137.438| |-----------------------------------------------------------------------------| r_work (start): 0.3784 rms_B_bonded: 2.12 r_work: 0.3596 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 10628 Z= 0.157 Angle : 0.617 17.006 14301 Z= 0.315 Chirality : 0.037 0.201 1644 Planarity : 0.003 0.037 1762 Dihedral : 11.033 76.171 1704 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.30 % Favored : 96.62 % Rotamer: Outliers : 1.92 % Allowed : 19.62 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.23 (0.23), residues: 1272 helix: 3.29 (0.14), residues: 1130 sheet: None (None), residues: 0 loop : -2.05 (0.51), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 118 TYR 0.019 0.002 TYR C 84 PHE 0.013 0.001 PHE E 209 TRP 0.019 0.001 TRP L 32 HIS 0.004 0.000 HIS A 151 Details of bonding type rmsd covalent geometry : bond 0.00362 (10628) covalent geometry : angle 0.61659 (14301) hydrogen bonds : bond 0.05318 ( 903) hydrogen bonds : angle 3.20466 ( 2700) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2455.89 seconds wall clock time: 42 minutes 46.82 seconds (2566.82 seconds total)