Starting phenix.real_space_refine on Wed Feb 4 01:08:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.cif Found real_map, /net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8yq6_39497/02_2026/8yq6_39497.map" } resolution = 2.9 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= 0.013 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: 4 Type Number sf(0) Gaussians S 35 5.16 5 C 5434 2.51 5 N 1313 2.21 5 O 1323 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8105 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 1588 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 203, 1580 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 44 Conformer: "B" Number of residues, atoms: 203, 1580 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1, 'HIS:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1, 'GLU:plan': 6} Unresolved non-hydrogen planarities: 44 bond proxies already assigned to first conformer: 1602 Chain: "D" Number of atoms: 1603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1603 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 199} Chain breaks: 1 Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 82 Unresolved non-hydrogen dihedrals: 60 Planarities with less than four sites: {'TYR:plan': 2, 'ASP:plan': 1, 'GLU:plan': 7} Unresolved non-hydrogen planarities: 45 Chain: "C" Number of atoms: 1646 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1638 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Conformer: "B" Number of residues, atoms: 206, 1638 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 28 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 bond proxies already assigned to first conformer: 1661 Chain: "B" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1638 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 1630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1630 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 43 Unresolved non-hydrogen angles: 50 Unresolved non-hydrogen dihedrals: 36 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 23 Time building chain proxies: 2.07, per 1000 atoms: 0.26 Number of scatterers: 8105 At special positions: 0 Unit cell: (78.09, 77.52, 118.56, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 35 16.00 O 1323 8.00 N 1313 7.00 C 5434 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: 0.44 Conformation dependent library (CDL) restraints added in 283.3 milliseconds 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1964 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 74.4% alpha, 5.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.15 Creating SS restraints... Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 27 through 35 removed outlier: 3.539A pdb=" N GLY E 35 " --> pdb=" O ARG E 31 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.640A pdb=" N PHE E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N TYR E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 88 Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 111 through 139 Processing helix chain 'E' and resid 141 through 173 removed outlier: 3.516A pdb=" N GLU E 173 " --> pdb=" O ARG E 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 208 Processing helix chain 'D' and resid 17 through 22 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 56 through 67 Processing helix chain 'D' and resid 77 through 88 removed outlier: 3.739A pdb=" N LEU D 81 " --> pdb=" O ASP D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 109 through 139 Processing helix chain 'D' and resid 141 through 173 Processing helix chain 'D' and resid 175 through 207 Processing helix chain 'C' and resid 17 through 22 Processing helix chain 'C' and resid 27 through 34 Processing helix chain 'C' and resid 55 through 67 removed outlier: 4.310A pdb=" N TYR C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 88 Processing helix chain 'C' and resid 90 through 104 Processing helix chain 'C' and resid 108 through 139 Processing helix chain 'C' and resid 141 through 173 Processing helix chain 'C' and resid 175 through 208 removed outlier: 3.558A pdb=" N LEU C 208 " --> pdb=" O LEU C 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 22 Processing helix chain 'B' and resid 27 through 34 Processing helix chain 'B' and resid 53 through 67 removed outlier: 3.785A pdb=" N ARG B 58 " --> pdb=" O GLY B 54 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N TYR B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 88 Processing helix chain 'B' and resid 90 through 105 Processing helix chain 'B' and resid 109 through 139 Processing helix chain 'B' and resid 141 through 173 Processing helix chain 'B' and resid 175 through 208 Processing helix chain 'A' and resid 18 through 22 Processing helix chain 'A' and resid 27 through 34 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.612A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ARG A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N TYR A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 88 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 108 through 139 Processing helix chain 'A' and resid 141 through 173 Processing helix chain 'A' and resid 175 through 208 removed outlier: 3.542A pdb=" N LEU A 208 " --> pdb=" O LEU A 204 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 17 removed outlier: 4.379A pdb=" N VAL E 40 " --> pdb=" O PHE E 49 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 16 removed outlier: 4.178A pdb=" N VAL D 40 " --> pdb=" O PHE D 49 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 12 through 16 removed outlier: 4.242A pdb=" N VAL C 40 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 17 removed outlier: 4.262A pdb=" N VAL B 40 " --> pdb=" O PHE B 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 12 through 17 removed outlier: 4.164A pdb=" N VAL A 40 " --> pdb=" O PHE A 49 " (cutoff:3.500A) 639 hydrogen bonds defined for protein. 1879 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: 0.82 Time building geometry restraints manager: 0.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2457 1.34 - 1.46: 1303 1.46 - 1.58: 4432 1.58 - 1.69: 2 1.69 - 1.81: 70 Bond restraints: 8264 Sorted by residual: bond pdb=" C ARG E 157 " pdb=" CA AARG E 157 " ideal model delta sigma weight residual 1.524 1.593 -0.069 1.32e-02 5.74e+03 2.75e+01 bond pdb=" C ARG C 165 " pdb=" O ARG C 165 " ideal model delta sigma weight residual 1.237 1.292 -0.055 1.17e-02 7.31e+03 2.24e+01 bond pdb=" C ARG E 157 " pdb=" O ARG E 157 " ideal model delta sigma weight residual 1.236 1.290 -0.054 1.15e-02 7.56e+03 2.19e+01 bond pdb=" C ARG C 165 " pdb=" CA AARG C 165 " ideal model delta sigma weight residual 1.523 1.577 -0.054 1.30e-02 5.92e+03 1.69e+01 bond pdb=" N ARG E 157 " pdb=" CA BARG E 157 " ideal model delta sigma weight residual 1.459 1.496 -0.036 1.20e-02 6.94e+03 9.23e+00 ... (remaining 8259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.55: 10864 1.55 - 3.10: 269 3.10 - 4.65: 49 4.65 - 6.20: 15 6.20 - 7.74: 4 Bond angle restraints: 11201 Sorted by residual: angle pdb=" O ARG C 165 " pdb=" C ARG C 165 " pdb=" CA BARG C 165 " ideal model delta sigma weight residual 120.55 127.51 -6.96 1.06e+00 8.90e-01 4.31e+01 angle pdb=" O ARG E 157 " pdb=" C ARG E 157 " pdb=" CA AARG E 157 " ideal model delta sigma weight residual 120.90 127.05 -6.15 1.07e+00 8.73e-01 3.30e+01 angle pdb=" O ARG E 157 " pdb=" C ARG E 157 " pdb=" CA BARG E 157 " ideal model delta sigma weight residual 120.90 126.93 -6.03 1.07e+00 8.73e-01 3.18e+01 angle pdb=" O ARG C 165 " pdb=" C ARG C 165 " pdb=" CA AARG C 165 " ideal model delta sigma weight residual 120.55 126.12 -5.57 1.06e+00 8.90e-01 2.76e+01 angle pdb=" N ARG C 165 " pdb=" CA BARG C 165 " pdb=" C ARG C 165 " ideal model delta sigma weight residual 111.28 116.21 -4.93 1.09e+00 8.42e-01 2.04e+01 ... (remaining 11196 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.11: 4441 15.11 - 30.21: 375 30.21 - 45.32: 81 45.32 - 60.42: 28 60.42 - 75.52: 4 Dihedral angle restraints: 4929 sinusoidal: 1912 harmonic: 3017 Sorted by residual: dihedral pdb=" CG ARG A 169 " pdb=" CD ARG A 169 " pdb=" NE ARG A 169 " pdb=" CZ ARG A 169 " ideal model delta sinusoidal sigma weight residual -180.00 -135.98 -44.02 2 1.50e+01 4.44e-03 1.03e+01 dihedral pdb=" CA ASP A 34 " pdb=" CB ASP A 34 " pdb=" CG ASP A 34 " pdb=" OD1 ASP A 34 " ideal model delta sinusoidal sigma weight residual -30.00 -84.28 54.28 1 2.00e+01 2.50e-03 9.99e+00 dihedral pdb=" CA MET D 97 " pdb=" C MET D 97 " pdb=" N GLU D 98 " pdb=" CA GLU D 98 " ideal model delta harmonic sigma weight residual 180.00 164.34 15.66 0 5.00e+00 4.00e-02 9.81e+00 ... (remaining 4926 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1010 0.042 - 0.084: 272 0.084 - 0.126: 79 0.126 - 0.168: 9 0.168 - 0.210: 3 Chirality restraints: 1373 Sorted by residual: chirality pdb=" CA ILE D 164 " pdb=" N ILE D 164 " pdb=" C ILE D 164 " pdb=" CB ILE D 164 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA GLU C 96 " pdb=" N GLU C 96 " pdb=" C GLU C 96 " pdb=" CB GLU C 96 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.98e-01 chirality pdb=" CA LEU D 158 " pdb=" N LEU D 158 " pdb=" C LEU D 158 " pdb=" CB LEU D 158 " both_signs ideal model delta sigma weight residual False 2.51 2.69 -0.18 2.00e-01 2.50e+01 7.78e-01 ... (remaining 1370 not shown) Planarity restraints: 1342 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU E 155 " 0.010 2.00e-02 2.50e+03 2.01e-02 4.06e+00 pdb=" C LEU E 155 " -0.035 2.00e-02 2.50e+03 pdb=" O LEU E 155 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL E 156 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ARG C 165 " 0.035 2.00e-02 2.50e+03 2.00e-02 4.01e+00 pdb=" O ARG C 165 " -0.013 2.00e-02 2.50e+03 pdb=" CA AARG C 165 " -0.010 2.00e-02 2.50e+03 pdb=" N VAL C 166 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PRO C 92 " -0.008 2.00e-02 2.50e+03 1.59e-02 2.53e+00 pdb=" C PRO C 92 " 0.028 2.00e-02 2.50e+03 pdb=" O PRO C 92 " -0.010 2.00e-02 2.50e+03 pdb=" N MET C 93 " -0.009 2.00e-02 2.50e+03 ... (remaining 1339 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1266 2.76 - 3.30: 8069 3.30 - 3.83: 14039 3.83 - 4.37: 16135 4.37 - 4.90: 27707 Nonbonded interactions: 67216 Sorted by model distance: nonbonded pdb=" OH TYR A 14 " pdb=" O GLY A 54 " model vdw 2.226 3.040 nonbonded pdb=" OD2 ASP C 51 " pdb=" OG SER B 17 " model vdw 2.306 3.040 nonbonded pdb=" O LEU B 18 " pdb=" OG1 THR B 22 " model vdw 2.306 3.040 nonbonded pdb=" NH2 ARG C 31 " pdb=" OE1 GLN C 89 " model vdw 2.308 3.120 nonbonded pdb=" O LEU C 18 " pdb=" OG1 THR C 22 " model vdw 2.319 3.040 ... (remaining 67211 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 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 45 or (resid 46 through 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 64 or (resid \ 65 and (name N or name CA or name C or name O or name CB )) or resid 66 through \ 67 or (resid 68 through 69 and (name N or name CA or name C or name O or name C \ B )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB )) or resid 75 through 81 or (resid 82 and (name N or name CA or \ name C or name O or name CB )) or resid 83 through 103 or (resid 104 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throu \ gh 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB )) or resid 142 through 156 or resid 158 through 164 or resid 166 through \ 174 or (resid 175 through 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 through 183 or (resid 184 through 185 and (name N or name C \ A or name C or name O or name CB )) or resid 186 through 208)) selection = (chain 'B' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 43 or (resid 44 through 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 64 or (resid \ 65 and (name N or name CA or name C or name O or name CB )) or resid 66 through \ 67 or (resid 68 through 69 and (name N or name CA or name C or name O or name C \ B )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB )) or resid 75 through 81 or (resid 82 and (name N or name CA or \ name C or name O or name CB )) or resid 83 through 103 or (resid 104 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throu \ gh 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB )) or resid 142 through 156 or resid 158 through 164 or resid 166 through \ 174 or (resid 175 through 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 through 184 or (resid 185 and (name N or name CA or name C \ or name O or name CB )) or resid 186 through 208)) selection = (chain 'C' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 44 or (resid 45 through 47 and (name \ N or name CA or name C or name O or name CB )) or resid 48 through 64 or (resid \ 65 and (name N or name CA or name C or name O or name CB )) or resid 66 through \ 67 or (resid 68 through 69 and (name N or name CA or name C or name O or name C \ B )) or resid 70 through 73 or (resid 74 and (name N or name CA or name C or nam \ e O or name CB )) or resid 75 through 81 or (resid 82 and (name N or name CA or \ name C or name O or name CB )) or resid 83 through 103 or (resid 104 and (name N \ or name CA or name C or name O or name CB )) or resid 110 through 112 or (resid \ 113 and (name N or name CA or name C or name O or name CB )) or resid 114 throu \ gh 139 or (resid 140 through 141 and (name N or name CA or name C or name O or n \ ame CB )) or resid 142 through 156 or resid 158 through 164 or resid 166 through \ 174 or (resid 175 through 181 and (name N or name CA or name C or name O or nam \ e CB )) or resid 182 through 183 or (resid 184 through 185 and (name N or name C \ A or name C or name O or name CB )) or resid 186 through 208)) selection = (chain 'D' and ((resid 1 through 3 and (name N or name CA or name C or name O or \ name CB )) or resid 4 through 43 or (resid 44 through 47 and (name N or name CA \ or name C or name O or name CB )) or resid 48 through 64 or (resid 65 and (name \ N or name CA or name C or name O or name CB )) or resid 66 through 67 or (resid \ 68 through 69 and (name N or name CA or name C or name O or name CB )) or resid \ 70 through 73 or (resid 74 and (name N or name CA or name C or name O or name C \ B )) or resid 75 through 104 or resid 110 through 156 or resid 158 through 164 o \ r resid 166 through 174 or (resid 175 through 181 and (name N or name CA or name \ C or name O or name CB )) or resid 182 through 184 or (resid 185 and (name N or \ name CA or name C or name O or name CB )) or resid 186 through 208)) selection = (chain 'E' and (resid 1 through 13 or (resid 14 and (name N or name CA or name C \ or name O or name CB )) or resid 15 through 72 or (resid 73 through 74 and (nam \ e N or name CA or name C or name O or name CB )) or resid 75 through 81 or (resi \ d 82 and (name N or name CA or name C or name O or name CB )) or resid 83 throug \ h 139 or (resid 140 through 141 and (name N or name CA or name C or name O or na \ me CB )) or resid 142 through 156 or resid 158 through 164 or resid 166 through \ 179 or (resid 180 through 181 and (name N or name CA or name C or name O or name \ CB )) or resid 182 through 208)) } 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=0.50 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: 8.820 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: 0.190 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.520 Find NCS groups from input model: 0.110 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8069 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 : 0.004 0.069 8264 Z= 0.235 Angle : 0.632 7.744 11201 Z= 0.388 Chirality : 0.043 0.210 1373 Planarity : 0.003 0.032 1342 Dihedral : 12.626 75.524 2965 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 1.22 % Allowed : 0.12 % Favored : 98.66 % 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: 2.57 (0.26), residues: 1008 helix: 2.22 (0.18), residues: 743 sheet: 3.03 (1.48), residues: 10 loop : 0.14 (0.38), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 52 TYR 0.011 0.002 TYR A 87 PHE 0.026 0.002 PHE E 163 TRP 0.006 0.001 TRP C 135 HIS 0.005 0.002 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8264) covalent geometry : angle 0.63228 (11201) hydrogen bonds : bond 0.10199 ( 639) hydrogen bonds : angle 4.53575 ( 1879) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 187 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: E 86 LYS cc_start: 0.7204 (tttm) cc_final: 0.6983 (ttmt) REVERT: E 117 LYS cc_start: 0.7708 (ttmt) cc_final: 0.6787 (tmtm) REVERT: D 2 ASN cc_start: 0.7761 (m-40) cc_final: 0.7500 (m110) REVERT: D 157 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7818 (ttm170) REVERT: C 117 LYS cc_start: 0.8040 (mtpp) cc_final: 0.7348 (tmtt) REVERT: C 169 ARG cc_start: 0.8001 (ttm-80) cc_final: 0.7555 (ttt-90) REVERT: B 138 LYS cc_start: 0.7545 (tmtt) cc_final: 0.6839 (mptt) REVERT: A 27 SER cc_start: 0.8587 (p) cc_final: 0.8379 (t) REVERT: A 117 LYS cc_start: 0.7895 (mtpt) cc_final: 0.7165 (tptt) REVERT: A 157 ARG cc_start: 0.7571 (mmm-85) cc_final: 0.7322 (ttt180) outliers start: 7 outliers final: 1 residues processed: 189 average time/residue: 0.5669 time to fit residues: 112.3734 Evaluate side-chains 132 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 130 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain B residue 161 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 10.0000 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.2980 chunk 45 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS E 91 GLN D 102 GLN A 46 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.159102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.128117 restraints weight = 20652.151| |-----------------------------------------------------------------------------| r_work (start): 0.3372 rms_B_bonded: 3.44 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3401 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3401 r_free = 0.3401 target_work(ls_wunit_k1) = 0.132 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3401 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8264 Z= 0.142 Angle : 0.499 7.591 11201 Z= 0.255 Chirality : 0.039 0.145 1373 Planarity : 0.003 0.028 1342 Dihedral : 4.719 57.326 1117 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 3.52 % Allowed : 8.63 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 3.31 (0.25), residues: 1008 helix: 2.76 (0.18), residues: 745 sheet: 3.12 (1.06), residues: 20 loop : 0.28 (0.40), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 52 TYR 0.016 0.002 TYR A 78 PHE 0.017 0.002 PHE C 163 TRP 0.006 0.001 TRP E 202 HIS 0.003 0.001 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00329 ( 8264) covalent geometry : angle 0.49887 (11201) hydrogen bonds : bond 0.04158 ( 639) hydrogen bonds : angle 3.49057 ( 1879) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 0.275 Fit side-chains REVERT: E 117 LYS cc_start: 0.7702 (ttmt) cc_final: 0.6860 (tmtm) REVERT: D 2 ASN cc_start: 0.8058 (m-40) cc_final: 0.7818 (m110) REVERT: D 157 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7688 (ttt180) REVERT: D 161 ARG cc_start: 0.8180 (OUTLIER) cc_final: 0.7596 (ttt180) REVERT: C 117 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7482 (tmtt) REVERT: C 169 ARG cc_start: 0.7955 (ttm-80) cc_final: 0.7568 (ttt-90) REVERT: B 96 GLU cc_start: 0.7605 (OUTLIER) cc_final: 0.7386 (mp0) REVERT: B 138 LYS cc_start: 0.7826 (tmtt) cc_final: 0.6797 (mptt) REVERT: B 161 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.6934 (mtm180) REVERT: B 175 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.5575 (mtmm) REVERT: A 24 TYR cc_start: 0.7599 (m-80) cc_final: 0.7250 (m-80) outliers start: 26 outliers final: 5 residues processed: 159 average time/residue: 0.5516 time to fit residues: 92.1535 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 69 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 81 optimal weight: 3.9990 chunk 6 optimal weight: 6.9990 chunk 57 optimal weight: 0.0170 chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 0.6980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 HIS D 102 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.160009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.128536 restraints weight = 17026.664| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 2.98 r_work: 0.3062 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3038 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3038 r_free = 0.3038 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3038 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8264 Z= 0.117 Angle : 0.449 5.827 11201 Z= 0.234 Chirality : 0.038 0.130 1373 Planarity : 0.003 0.028 1342 Dihedral : 4.252 57.976 1113 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 3.40 % Allowed : 12.03 % Favored : 84.57 % 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: 3.67 (0.25), residues: 1008 helix: 3.04 (0.18), residues: 748 sheet: 3.31 (1.04), residues: 20 loop : 0.31 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 157 TYR 0.018 0.001 TYR A 87 PHE 0.013 0.001 PHE C 163 TRP 0.007 0.001 TRP D 202 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00264 ( 8264) covalent geometry : angle 0.44862 (11201) hydrogen bonds : bond 0.03759 ( 639) hydrogen bonds : angle 3.28980 ( 1879) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7795 (ttmt) cc_final: 0.6902 (tmtm) REVERT: D 18 LEU cc_start: 0.8130 (OUTLIER) cc_final: 0.7905 (mt) REVERT: D 157 ARG cc_start: 0.8793 (OUTLIER) cc_final: 0.8331 (ttm110) REVERT: D 161 ARG cc_start: 0.8420 (OUTLIER) cc_final: 0.7883 (ttt180) REVERT: C 55 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8197 (mt0) REVERT: C 95 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8688 (mp) REVERT: C 117 LYS cc_start: 0.8395 (mtpp) cc_final: 0.7449 (tmtt) REVERT: C 169 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7495 (ttt-90) REVERT: B 96 GLU cc_start: 0.8158 (OUTLIER) cc_final: 0.7752 (mp0) REVERT: B 138 LYS cc_start: 0.7951 (tmtt) cc_final: 0.6561 (mptt) REVERT: B 161 ARG cc_start: 0.8132 (mtp-110) cc_final: 0.7055 (mtm180) REVERT: A 24 TYR cc_start: 0.7483 (m-80) cc_final: 0.7139 (m-80) outliers start: 25 outliers final: 5 residues processed: 146 average time/residue: 0.6122 time to fit residues: 93.9248 Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 96 GLU Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 96 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.152672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120861 restraints weight = 20589.009| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 3.58 r_work (final): 0.3267 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.121 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 8264 Z= 0.199 Angle : 0.559 7.825 11201 Z= 0.283 Chirality : 0.041 0.154 1373 Planarity : 0.003 0.028 1342 Dihedral : 4.606 55.676 1113 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 4.37 % Allowed : 12.39 % Favored : 83.23 % 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: 3.31 (0.25), residues: 1008 helix: 2.80 (0.17), residues: 738 sheet: 2.95 (0.82), residues: 30 loop : 0.09 (0.41), residues: 240 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 157 TYR 0.016 0.002 TYR A 87 PHE 0.020 0.002 PHE C 163 TRP 0.008 0.001 TRP D 202 HIS 0.005 0.002 HIS C 12 Details of bonding type rmsd covalent geometry : bond 0.00483 ( 8264) covalent geometry : angle 0.55873 (11201) hydrogen bonds : bond 0.04659 ( 639) hydrogen bonds : angle 3.60118 ( 1879) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 132 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7740 (ttmt) cc_final: 0.6890 (tmtm) REVERT: D 117 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7566 (mttm) REVERT: D 157 ARG cc_start: 0.8122 (OUTLIER) cc_final: 0.7681 (ttt180) REVERT: D 161 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7683 (ttt180) REVERT: C 55 GLN cc_start: 0.8570 (OUTLIER) cc_final: 0.7865 (mt0) REVERT: C 95 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8599 (mp) REVERT: C 117 LYS cc_start: 0.8429 (mtpp) cc_final: 0.7579 (tmtt) REVERT: C 169 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7530 (ttt-90) REVERT: B 40 VAL cc_start: 0.8679 (OUTLIER) cc_final: 0.8249 (p) REVERT: B 161 ARG cc_start: 0.7731 (OUTLIER) cc_final: 0.7011 (mtm180) REVERT: A 24 TYR cc_start: 0.7557 (m-80) cc_final: 0.7209 (m-80) outliers start: 33 outliers final: 5 residues processed: 150 average time/residue: 0.5585 time to fit residues: 88.2529 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 126 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 49 optimal weight: 0.6980 chunk 77 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 70 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 45 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 97 optimal weight: 8.9990 chunk 24 optimal weight: 0.2980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.153998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.121800 restraints weight = 17646.555| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 3.06 r_work: 0.2937 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8475 moved from start: 0.2741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8264 Z= 0.144 Angle : 0.494 8.456 11201 Z= 0.253 Chirality : 0.038 0.133 1373 Planarity : 0.003 0.028 1342 Dihedral : 4.411 55.451 1113 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.80 % Favored : 99.20 % Rotamer: Outliers : 3.04 % Allowed : 15.07 % Favored : 81.90 % 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: 3.45 (0.25), residues: 1008 helix: 2.90 (0.17), residues: 745 sheet: 3.11 (0.82), residues: 30 loop : 0.05 (0.41), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 52 TYR 0.012 0.001 TYR A 87 PHE 0.015 0.002 PHE C 163 TRP 0.008 0.001 TRP D 202 HIS 0.003 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 8264) covalent geometry : angle 0.49383 (11201) hydrogen bonds : bond 0.04079 ( 639) hydrogen bonds : angle 3.43920 ( 1879) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 0.243 Fit side-chains revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7859 (ttmt) cc_final: 0.6947 (tmtm) REVERT: D 26 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7847 (mm-30) REVERT: D 117 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7510 (mttm) REVERT: D 157 ARG cc_start: 0.8675 (OUTLIER) cc_final: 0.8137 (ttt180) REVERT: D 161 ARG cc_start: 0.8366 (OUTLIER) cc_final: 0.7921 (ttt180) REVERT: C 55 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.8441 (mt0) REVERT: C 95 LEU cc_start: 0.8794 (OUTLIER) cc_final: 0.8512 (mp) REVERT: C 117 LYS cc_start: 0.8498 (mtpp) cc_final: 0.7405 (tmtt) REVERT: C 169 ARG cc_start: 0.8195 (ttm-80) cc_final: 0.7636 (ttt-90) REVERT: B 55 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8214 (mt0) REVERT: B 161 ARG cc_start: 0.8243 (mtp-110) cc_final: 0.7043 (mtm180) REVERT: A 24 TYR cc_start: 0.7503 (m-80) cc_final: 0.7148 (m-80) REVERT: A 117 LYS cc_start: 0.8149 (mtpt) cc_final: 0.7212 (tptt) outliers start: 22 outliers final: 5 residues processed: 147 average time/residue: 0.6190 time to fit residues: 95.3176 Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 130 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 34 optimal weight: 0.6980 chunk 67 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 53 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.152461 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.121283 restraints weight = 14748.140| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 2.50 r_work: 0.2992 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8264 Z= 0.170 Angle : 0.528 7.493 11201 Z= 0.270 Chirality : 0.039 0.144 1373 Planarity : 0.003 0.029 1342 Dihedral : 4.470 54.163 1113 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Rotamer: Outliers : 3.28 % Allowed : 15.80 % Favored : 80.92 % 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: 3.30 (0.25), residues: 1008 helix: 2.81 (0.17), residues: 739 sheet: 3.03 (0.82), residues: 30 loop : -0.01 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 52 TYR 0.013 0.002 TYR B 59 PHE 0.017 0.002 PHE C 163 TRP 0.009 0.001 TRP D 202 HIS 0.004 0.001 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 8264) covalent geometry : angle 0.52764 (11201) hydrogen bonds : bond 0.04346 ( 639) hydrogen bonds : angle 3.57059 ( 1879) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7819 (ttmt) cc_final: 0.6914 (tmtm) REVERT: D 26 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7765 (mm-30) REVERT: D 117 LYS cc_start: 0.7874 (mtmt) cc_final: 0.7558 (mttm) REVERT: D 157 ARG cc_start: 0.8593 (OUTLIER) cc_final: 0.8060 (ttt180) REVERT: D 161 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7900 (ttt180) REVERT: C 55 GLN cc_start: 0.8998 (OUTLIER) cc_final: 0.8415 (mt0) REVERT: C 95 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8515 (mp) REVERT: C 117 LYS cc_start: 0.8490 (mtpp) cc_final: 0.7409 (tmtt) REVERT: C 169 ARG cc_start: 0.8193 (ttm-80) cc_final: 0.7647 (ttt-90) REVERT: B 55 GLN cc_start: 0.8628 (OUTLIER) cc_final: 0.8154 (mt0) REVERT: B 161 ARG cc_start: 0.8182 (OUTLIER) cc_final: 0.7080 (mtm180) REVERT: B 175 LYS cc_start: 0.6729 (OUTLIER) cc_final: 0.5815 (mtmm) REVERT: A 24 TYR cc_start: 0.7503 (m-80) cc_final: 0.7152 (m-80) outliers start: 24 outliers final: 7 residues processed: 143 average time/residue: 0.6299 time to fit residues: 94.1619 Evaluate side-chains 140 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 125 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 18 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain C residue 55 GLN Chi-restraints excluded: chain C residue 95 LEU Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 175 LYS Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 30 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 8 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 50 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.151955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.118716 restraints weight = 15595.097| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 2.86 r_work: 0.2951 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2951 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.059 8264 Z= 0.346 Angle : 0.718 9.506 11201 Z= 0.361 Chirality : 0.047 0.196 1373 Planarity : 0.005 0.045 1342 Dihedral : 5.089 51.978 1113 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.52 % Allowed : 16.40 % Favored : 80.07 % 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: 2.37 (0.25), residues: 1008 helix: 2.12 (0.17), residues: 736 sheet: 2.95 (0.85), residues: 30 loop : -0.35 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 28 TYR 0.018 0.003 TYR A 87 PHE 0.026 0.003 PHE C 163 TRP 0.014 0.002 TRP D 202 HIS 0.009 0.003 HIS B 12 Details of bonding type rmsd covalent geometry : bond 0.00867 ( 8264) covalent geometry : angle 0.71836 (11201) hydrogen bonds : bond 0.05631 ( 639) hydrogen bonds : angle 4.07884 ( 1879) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.240 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7906 (ttmt) cc_final: 0.6875 (tmtm) REVERT: D 26 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7687 (mm-30) REVERT: D 117 LYS cc_start: 0.7862 (OUTLIER) cc_final: 0.7587 (mttm) REVERT: D 157 ARG cc_start: 0.8690 (OUTLIER) cc_final: 0.8257 (ttt180) REVERT: D 161 ARG cc_start: 0.8311 (OUTLIER) cc_final: 0.7912 (ttt180) REVERT: C 117 LYS cc_start: 0.8558 (mtpp) cc_final: 0.7436 (tmtt) REVERT: C 169 ARG cc_start: 0.8170 (ttm-80) cc_final: 0.7606 (ttt-90) REVERT: B 40 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8355 (p) REVERT: B 55 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8200 (mt0) REVERT: B 161 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6997 (mtm110) REVERT: A 24 TYR cc_start: 0.7572 (m-80) cc_final: 0.7083 (m-80) REVERT: A 95 LEU cc_start: 0.7344 (tt) cc_final: 0.6762 (mp) outliers start: 26 outliers final: 7 residues processed: 141 average time/residue: 0.5951 time to fit residues: 87.9961 Evaluate side-chains 140 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 126 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 ILE Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Chi-restraints excluded: chain A residue 71 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 78 optimal weight: 0.8980 chunk 40 optimal weight: 0.2980 chunk 61 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 77 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.154111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.121541 restraints weight = 12673.533| |-----------------------------------------------------------------------------| r_work (start): 0.3272 rms_B_bonded: 1.96 r_work: 0.3031 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3021 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3021 r_free = 0.3021 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3021 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.3132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 8264 Z= 0.132 Angle : 0.509 9.328 11201 Z= 0.261 Chirality : 0.039 0.141 1373 Planarity : 0.003 0.031 1342 Dihedral : 4.514 52.905 1113 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 2.92 % Allowed : 17.74 % Favored : 79.34 % 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: 3.13 (0.25), residues: 1008 helix: 2.71 (0.18), residues: 744 sheet: 3.05 (0.84), residues: 30 loop : -0.28 (0.40), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 28 TYR 0.013 0.001 TYR A 87 PHE 0.013 0.001 PHE C 163 TRP 0.012 0.001 TRP E 100 HIS 0.003 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8264) covalent geometry : angle 0.50885 (11201) hydrogen bonds : bond 0.04075 ( 639) hydrogen bonds : angle 3.60270 ( 1879) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 0.208 Fit side-chains revert: symmetry clash REVERT: E 117 LYS cc_start: 0.7804 (ttmt) cc_final: 0.6888 (tmtm) REVERT: D 56 MET cc_start: 0.8801 (mmp) cc_final: 0.7503 (mmt) REVERT: D 80 LEU cc_start: 0.8094 (mp) cc_final: 0.7419 (tp) REVERT: D 98 GLU cc_start: 0.8081 (mt-10) cc_final: 0.7876 (mt-10) REVERT: D 117 LYS cc_start: 0.7806 (mtmt) cc_final: 0.7534 (mttm) REVERT: D 157 ARG cc_start: 0.8557 (OUTLIER) cc_final: 0.7957 (ttt90) REVERT: D 161 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7844 (ttt180) REVERT: C 117 LYS cc_start: 0.8456 (mtpp) cc_final: 0.7316 (tmtt) REVERT: C 169 ARG cc_start: 0.8178 (ttm-80) cc_final: 0.7600 (ttt-90) REVERT: B 55 GLN cc_start: 0.8573 (OUTLIER) cc_final: 0.8084 (mt0) REVERT: B 96 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7756 (mm-30) REVERT: B 161 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.6963 (mtm180) REVERT: A 24 TYR cc_start: 0.7469 (m-80) cc_final: 0.6979 (m-80) REVERT: A 117 LYS cc_start: 0.8112 (mtpt) cc_final: 0.7543 (mtpp) REVERT: A 138 LYS cc_start: 0.8020 (tttt) cc_final: 0.7483 (ttmt) outliers start: 21 outliers final: 4 residues processed: 147 average time/residue: 0.6003 time to fit residues: 92.2151 Evaluate side-chains 142 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 134 time to evaluate : 0.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 70 optimal weight: 6.9990 chunk 59 optimal weight: 0.5980 chunk 84 optimal weight: 8.9990 chunk 54 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 60 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 82 optimal weight: 3.9990 chunk 80 optimal weight: 0.4980 chunk 49 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.155420 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.122357 restraints weight = 19609.894| |-----------------------------------------------------------------------------| r_work (start): 0.3295 rms_B_bonded: 3.73 r_work: 0.2958 rms_B_bonded: 4.73 restraints_weight: 0.5000 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2933 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2933 r_free = 0.2933 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2933 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8264 Z= 0.124 Angle : 0.491 9.250 11201 Z= 0.254 Chirality : 0.038 0.192 1373 Planarity : 0.003 0.033 1342 Dihedral : 4.286 51.125 1113 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.07 % Allowed : 18.47 % Favored : 79.47 % 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: 3.33 (0.25), residues: 1008 helix: 2.85 (0.18), residues: 747 sheet: 3.19 (0.81), residues: 30 loop : -0.21 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 165 TYR 0.010 0.001 TYR A 87 PHE 0.012 0.001 PHE D 33 TRP 0.011 0.001 TRP E 100 HIS 0.002 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 8264) covalent geometry : angle 0.49133 (11201) hydrogen bonds : bond 0.03849 ( 639) hydrogen bonds : angle 3.53905 ( 1879) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 134 time to evaluate : 0.310 Fit side-chains REVERT: E 117 LYS cc_start: 0.7803 (ttmt) cc_final: 0.6926 (tmtm) REVERT: D 117 LYS cc_start: 0.7858 (mtmt) cc_final: 0.7511 (mttm) REVERT: D 157 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.8289 (ttt180) REVERT: D 161 ARG cc_start: 0.8421 (OUTLIER) cc_final: 0.7988 (ttt180) REVERT: D 206 LYS cc_start: 0.7925 (mptt) cc_final: 0.7639 (mtpp) REVERT: C 117 LYS cc_start: 0.8482 (mtpp) cc_final: 0.7330 (tmtt) REVERT: C 169 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7598 (ttt-90) REVERT: B 55 GLN cc_start: 0.8646 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: B 161 ARG cc_start: 0.8235 (OUTLIER) cc_final: 0.7052 (mtm180) REVERT: A 24 TYR cc_start: 0.7461 (m-80) cc_final: 0.7144 (m-80) outliers start: 14 outliers final: 6 residues processed: 140 average time/residue: 0.5729 time to fit residues: 84.1798 Evaluate side-chains 143 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 133 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 77 ASP Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 43 optimal weight: 0.3980 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.153735 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.120879 restraints weight = 12064.395| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.85 r_work: 0.3070 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2934 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2912 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2912 r_free = 0.2912 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2912 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8264 Z= 0.164 Angle : 0.546 10.346 11201 Z= 0.279 Chirality : 0.040 0.212 1373 Planarity : 0.003 0.032 1342 Dihedral : 4.380 50.346 1113 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.82 % Allowed : 18.71 % Favored : 79.47 % 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: 3.20 (0.25), residues: 1008 helix: 2.75 (0.18), residues: 746 sheet: 3.02 (0.81), residues: 30 loop : -0.23 (0.40), residues: 232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 165 TYR 0.015 0.002 TYR C 59 PHE 0.016 0.002 PHE C 163 TRP 0.013 0.001 TRP E 100 HIS 0.004 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8264) covalent geometry : angle 0.54588 (11201) hydrogen bonds : bond 0.04231 ( 639) hydrogen bonds : angle 3.65279 ( 1879) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2016 Ramachandran restraints generated. 1008 Oldfield, 0 Emsley, 1008 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 129 time to evaluate : 0.324 Fit side-chains REVERT: E 117 LYS cc_start: 0.7819 (ttmt) cc_final: 0.6921 (tmtm) REVERT: D 117 LYS cc_start: 0.7862 (mtmt) cc_final: 0.7500 (mttm) REVERT: D 157 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8302 (ttt180) REVERT: D 161 ARG cc_start: 0.8434 (OUTLIER) cc_final: 0.8001 (ttt180) REVERT: D 206 LYS cc_start: 0.7891 (mptt) cc_final: 0.7584 (mtpp) REVERT: C 117 LYS cc_start: 0.8516 (mtpp) cc_final: 0.7368 (tmtt) REVERT: C 169 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7616 (ttt-90) REVERT: B 55 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.8252 (mt0) REVERT: B 161 ARG cc_start: 0.8260 (OUTLIER) cc_final: 0.7065 (mtm180) REVERT: A 24 TYR cc_start: 0.7491 (m-80) cc_final: 0.7205 (m-80) REVERT: A 165 ARG cc_start: 0.7589 (ttt90) cc_final: 0.7187 (ttt-90) outliers start: 12 outliers final: 5 residues processed: 135 average time/residue: 0.6041 time to fit residues: 85.4064 Evaluate side-chains 138 residues out of total 888 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 129 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 95 LEU Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 101 LYS Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain D residue 161 ARG Chi-restraints excluded: chain B residue 55 GLN Chi-restraints excluded: chain B residue 161 ARG Chi-restraints excluded: chain B residue 188 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 89 optimal weight: 0.8980 chunk 90 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 10 optimal weight: 9.9990 chunk 52 optimal weight: 0.5980 chunk 98 optimal weight: 1.9990 chunk 64 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.154564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.121190 restraints weight = 13519.704| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.24 r_work: 0.3012 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 moved from start: 0.3200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8264 Z= 0.140 Angle : 0.526 10.051 11201 Z= 0.270 Chirality : 0.040 0.243 1373 Planarity : 0.003 0.033 1342 Dihedral : 4.297 49.881 1113 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 1.70 % Allowed : 18.96 % Favored : 79.34 % 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: 3.30 (0.25), residues: 1008 helix: 2.83 (0.18), residues: 747 sheet: 3.20 (0.82), residues: 30 loop : -0.23 (0.40), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 165 TYR 0.011 0.001 TYR D 78 PHE 0.013 0.001 PHE D 33 TRP 0.013 0.001 TRP E 100 HIS 0.003 0.001 HIS C 6 Details of bonding type rmsd covalent geometry : bond 0.00325 ( 8264) covalent geometry : angle 0.52612 (11201) hydrogen bonds : bond 0.04002 ( 639) hydrogen bonds : angle 3.58074 ( 1879) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2709.18 seconds wall clock time: 46 minutes 45.31 seconds (2805.31 seconds total)