Starting phenix.real_space_refine on Wed Feb 4 00:03:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m05_63538/02_2026/9m05_63538.map" } resolution = 3.72 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= 0.009 sd= 0.128 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 I 2 10.91 5 S 35 5.16 5 C 5352 2.51 5 N 1289 2.21 5 O 1303 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s 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: 7981 Number of models: 1 Model: "" Number of chains: 7 Chain: "E" Number of atoms: 1577 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1577 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain breaks: 2 Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 48 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 36 Chain: "D" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1634 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 198} Chain breaks: 1 Unresolved non-hydrogen bonds: 26 Unresolved non-hydrogen angles: 31 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 2, 'GLU:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "C" Number of atoms: 1656 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 206, 1649 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 Conformer: "B" Number of residues, atoms: 206, 1649 Classifications: {'peptide': 206} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 5, 'TRANS': 200} Chain breaks: 1 Unresolved non-hydrogen bonds: 29 Unresolved non-hydrogen angles: 34 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 3, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 13 bond proxies already assigned to first conformer: 1674 Chain: "B" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1637 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: 41 Unresolved non-hydrogen angles: 47 Unresolved non-hydrogen dihedrals: 35 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 14 Chain: "A" Number of atoms: 1475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1475 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 2 Unresolved non-hydrogen bonds: 55 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 44 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3} Unresolved non-hydrogen planarities: 26 Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'IOD': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'IOD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.91, per 1000 atoms: 0.24 Number of scatterers: 7981 At special positions: 0 Unit cell: (79.351, 80.438, 120.657, 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) I 2 52.95 S 35 16.00 O 1303 8.00 N 1289 7.00 C 5352 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: 0.83 Conformation dependent library (CDL) restraints added in 365.1 milliseconds 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1920 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 5 sheets defined 76.2% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'E' and resid 18 through 22 Processing helix chain 'E' and resid 27 through 34 Processing helix chain 'E' and resid 53 through 67 removed outlier: 3.847A pdb=" N PHE E 57 " --> pdb=" O ASP E 53 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ARG E 58 " --> pdb=" O GLY E 54 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N TYR E 59 " --> pdb=" O GLN E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 77 through 89 Processing helix chain 'E' and resid 90 through 104 Processing helix chain 'E' and resid 109 through 139 Processing helix chain 'E' and resid 141 through 172 Processing helix chain 'E' and resid 175 through 208 Processing helix chain 'D' and resid 18 through 22 Processing helix chain 'D' and resid 27 through 34 Processing helix chain 'D' and resid 55 through 67 removed outlier: 4.162A pdb=" N TYR D 59 " --> pdb=" O GLN D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 89 Processing helix chain 'D' and resid 90 through 104 Processing helix chain 'D' and resid 110 through 139 Processing helix chain 'D' and resid 141 through 173 Processing helix chain 'D' and resid 175 through 208 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: 4.156A pdb=" N TYR C 59 " --> pdb=" O GLN C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 77 through 89 Processing helix chain 'C' and resid 90 through 105 Processing helix chain 'C' and resid 109 through 139 Processing helix chain 'C' and resid 141 through 174 Processing helix chain 'C' and resid 175 through 208 removed outlier: 3.539A 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 55 through 67 removed outlier: 4.205A pdb=" N TYR B 59 " --> pdb=" O GLN B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 77 through 89 Processing helix chain 'B' and resid 90 through 105 Processing helix chain 'B' and resid 109 through 140 Processing helix chain 'B' and resid 141 through 172 Processing helix chain 'B' and resid 175 through 208 Processing helix chain 'A' and resid 17 through 22 removed outlier: 3.512A pdb=" N THR A 22 " --> pdb=" O LEU A 18 " (cutoff:3.500A) Processing helix chain 'A' and resid 27 through 33 Processing helix chain 'A' and resid 53 through 67 removed outlier: 3.760A pdb=" N PHE A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N TYR A 59 " --> pdb=" O GLN A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 77 through 89 Processing helix chain 'A' and resid 90 through 104 Processing helix chain 'A' and resid 110 through 139 Processing helix chain 'A' and resid 141 through 172 Processing helix chain 'A' and resid 175 through 208 Processing sheet with id=AA1, first strand: chain 'E' and resid 12 through 17 removed outlier: 3.573A pdb=" N TYR E 48 " --> pdb=" O HIS E 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 12 through 17 removed outlier: 4.426A 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 Processing sheet with id=AA4, first strand: chain 'B' and resid 12 through 17 Processing sheet with id=AA5, first strand: chain 'A' and resid 12 through 14 636 hydrogen bonds defined for protein. 1878 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: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2414 1.35 - 1.46: 1876 1.46 - 1.58: 3775 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8135 Sorted by residual: bond pdb=" CA ARG C 161 " pdb=" CB AARG C 161 " ideal model delta sigma weight residual 1.528 1.450 0.079 1.56e-02 4.11e+03 2.55e+01 bond pdb=" CA ARG D 161 " pdb=" C ARG D 161 " ideal model delta sigma weight residual 1.524 1.458 0.066 1.32e-02 5.74e+03 2.49e+01 bond pdb=" N ARG B 161 " pdb=" CA ARG B 161 " ideal model delta sigma weight residual 1.459 1.406 0.053 1.21e-02 6.83e+03 1.89e+01 bond pdb=" N ARG E 157 " pdb=" CA ARG E 157 " ideal model delta sigma weight residual 1.459 1.500 -0.041 1.21e-02 6.83e+03 1.15e+01 bond pdb=" N ARG D 161 " pdb=" CA ARG D 161 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.39e+00 ... (remaining 8130 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 10819 1.84 - 3.67: 160 3.67 - 5.51: 18 5.51 - 7.35: 7 7.35 - 9.19: 4 Bond angle restraints: 11008 Sorted by residual: angle pdb=" N ARG C 161 " pdb=" CA ARG C 161 " pdb=" CB AARG C 161 " ideal model delta sigma weight residual 110.12 119.31 -9.19 1.47e+00 4.63e-01 3.91e+01 angle pdb=" N ARG E 157 " pdb=" CA ARG E 157 " pdb=" CB ARG E 157 " ideal model delta sigma weight residual 110.12 117.86 -7.74 1.47e+00 4.63e-01 2.77e+01 angle pdb=" N ARG C 161 " pdb=" CA ARG C 161 " pdb=" CB BARG C 161 " ideal model delta sigma weight residual 110.12 114.56 -4.44 1.47e+00 4.63e-01 9.11e+00 angle pdb=" N ARG B 157 " pdb=" CA ARG B 157 " pdb=" C ARG B 157 " ideal model delta sigma weight residual 111.07 107.88 3.19 1.07e+00 8.73e-01 8.87e+00 angle pdb=" N ARG A 157 " pdb=" CA ARG A 157 " pdb=" C ARG A 157 " ideal model delta sigma weight residual 111.07 107.96 3.11 1.07e+00 8.73e-01 8.47e+00 ... (remaining 11003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.07: 4301 16.07 - 32.14: 418 32.14 - 48.21: 104 48.21 - 64.29: 18 64.29 - 80.36: 7 Dihedral angle restraints: 4848 sinusoidal: 1902 harmonic: 2946 Sorted by residual: dihedral pdb=" N ARG C 161 " pdb=" C ARG C 161 " pdb=" CA ARG C 161 " pdb=" CB AARG C 161 " ideal model delta harmonic sigma weight residual 122.80 135.40 -12.60 0 2.50e+00 1.60e-01 2.54e+01 dihedral pdb=" C ARG C 161 " pdb=" N ARG C 161 " pdb=" CA ARG C 161 " pdb=" CB AARG C 161 " ideal model delta harmonic sigma weight residual -122.60 -131.92 9.32 0 2.50e+00 1.60e-01 1.39e+01 dihedral pdb=" N ARG E 157 " pdb=" C ARG E 157 " pdb=" CA ARG E 157 " pdb=" CB ARG E 157 " ideal model delta harmonic sigma weight residual 122.80 131.20 -8.40 0 2.50e+00 1.60e-01 1.13e+01 ... (remaining 4845 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 1306 0.103 - 0.205: 27 0.205 - 0.308: 1 0.308 - 0.410: 0 0.410 - 0.513: 1 Chirality restraints: 1335 Sorted by residual: chirality pdb=" CA ARG C 161 " pdb=" N ARG C 161 " pdb=" C ARG C 161 " pdb=" CB AARG C 161 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.57e+00 chirality pdb=" CA ARG D 161 " pdb=" N ARG D 161 " pdb=" C ARG D 161 " pdb=" CB ARG D 161 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.97e+00 chirality pdb=" CA ARG E 157 " pdb=" N ARG E 157 " pdb=" C ARG E 157 " pdb=" CB ARG E 157 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 ... (remaining 1332 not shown) Planarity restraints: 1317 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU E 37 " -0.031 5.00e-02 4.00e+02 4.53e-02 3.29e+00 pdb=" N PRO E 38 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO E 38 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO E 38 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 71 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.23e+00 pdb=" N PRO A 72 " 0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 72 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 72 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 161 " 0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C ARG A 161 " -0.024 2.00e-02 2.50e+03 pdb=" O ARG A 161 " 0.009 2.00e-02 2.50e+03 pdb=" N PHE A 162 " 0.008 2.00e-02 2.50e+03 ... (remaining 1314 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.82: 2189 2.82 - 3.35: 8399 3.35 - 3.89: 13489 3.89 - 4.42: 14649 4.42 - 4.96: 24925 Nonbonded interactions: 63651 Sorted by model distance: nonbonded pdb=" O GLU E 26 " pdb=" NH2 ARG E 31 " model vdw 2.285 3.120 nonbonded pdb=" NH1 ARG C 65 " pdb=" OD1 ASP B 51 " model vdw 2.401 3.120 nonbonded pdb=" N GLU C 177 " pdb=" OE1 GLU C 177 " model vdw 2.427 3.120 nonbonded pdb=" O LEU A 80 " pdb=" OE1 GLU A 84 " model vdw 2.429 3.040 nonbonded pdb=" O ALA B 125 " pdb=" CG1 VAL B 128 " model vdw 2.433 3.460 ... (remaining 63646 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 6 through 25 or (resid 26 through 27 and (name N or name C \ A or name C or name O or name CB )) or resid 28 through 76 or (resid 77 and (nam \ e N or name CA or name C or name O or name CB )) or resid 78 through 112 or (res \ id 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thr \ ough 160 or resid 162 through 175 or (resid 176 through 180 and (name N or name \ CA or name C or name O or name CB )) or resid 181 through 183 or (resid 184 and \ (name N or name CA or name C or name O or name CB )) or resid 185 through 205 or \ (resid 206 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB or name OX \ T)))) selection = (chain 'B' and (resid 6 through 17 or (resid 18 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 26 or (resi \ d 27 and (name N or name CA or name C or name O or name CB )) or resid 28 throug \ h 31 or (resid 32 and (name N or name CA or name C or name O or name CB )) or re \ sid 33 or resid 47 through 64 or (resid 65 and (name N or name CA or name C or n \ ame O or name CB )) or resid 66 through 67 or (resid 68 and (name N or name CA o \ r name C or name O or name CB )) or resid 69 through 73 or (resid 74 and (name N \ or name CA or name C or name O or name CB )) or resid 75 through 76 or (resid 7 \ 7 and (name N or name CA or name C or name O or name CB )) or resid 78 through 1 \ 03 or (resid 104 and (name N or name CA or name C or name O or name CB )) or res \ id 109 through 112 or (resid 113 and (name N or name CA or name C or name O or n \ ame CB )) or resid 114 through 139 or (resid 140 through 141 and (name N or name \ CA or name C or name O or name CB )) or resid 142 through 160 or resid 162 thro \ ugh 167 or (resid 168 and (name N or name CA or name C or name O or name CB )) o \ r resid 169 through 175 or (resid 176 through 180 and (name N or name CA or name \ C or name O or name CB )) or resid 181 through 183 or (resid 184 and (name N or \ name CA or name C or name O or name CB )) or resid 185 through 208)) selection = (chain 'C' and (resid 6 through 17 or (resid 18 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 25 or (resi \ d 26 through 27 and (name N or name CA or name C or name O or name CB )) or resi \ d 28 through 31 or (resid 32 and (name N or name CA or name C or name O or name \ CB )) or resid 33 or resid 47 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 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 through 73 or (resid 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 76 \ or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 103 or (resid 104 and (name N or name CA or name C or name O or name C \ B )) or resid 109 through 137 or (resid 138 through 141 and (name N or name CA o \ r name C or name O or name CB )) or resid 142 through 160 or resid 162 through 1 \ 67 or (resid 168 and (name N or name CA or name C or name O or name CB )) or res \ id 169 through 171 or (resid 172 and (name N or name CA or name C or name O or n \ ame CB )) or resid 173 through 175 or (resid 176 through 180 and (name N or name \ CA or name C or name O or name CB )) or resid 181 through 207 or (resid 208 and \ (name N or name CA or name C or name O or name CB or name OXT)))) selection = (chain 'D' and (resid 6 through 17 or (resid 18 through 19 and (name N or name C \ A or name C or name O or name CB )) or resid 20 or (resid 21 through 22 and (nam \ e N or name CA or name C or name O or name CB )) or resid 23 through 25 or (resi \ d 26 through 27 and (name N or name CA or name C or name O or name CB )) or resi \ d 28 through 31 or (resid 32 and (name N or name CA or name C or name O or name \ CB )) or resid 33 or resid 47 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 and (name N o \ r name CA or name C or name O or name CB )) or resid 69 through 73 or (resid 74 \ and (name N or name CA or name C or name O or name CB )) or resid 75 through 76 \ or (resid 77 and (name N or name CA or name C or name O or name CB )) or resid 7 \ 8 through 102 or (resid 103 through 104 and (name N or name CA or name C or name \ O or name CB )) or resid 109 through 112 or (resid 113 and (name N or name CA o \ r name C or name O or name CB )) or resid 114 through 137 or (resid 138 through \ 141 and (name N or name CA or name C or name O or name CB )) or resid 142 throug \ h 160 or resid 162 through 167 or (resid 168 and (name N or name CA or name C or \ name O or name CB )) or resid 169 through 171 or (resid 172 and (name N or name \ CA or name C or name O or name CB )) or resid 173 through 177 or (resid 178 thr \ ough 180 and (name N or name CA or name C or name O or name CB )) or resid 181 t \ hrough 207 or (resid 208 and (name N or name CA or name C or name O or name CB o \ r name OXT)))) selection = (chain 'E' and (resid 6 through 20 or (resid 21 through 22 and (name N or name C \ A or name C or name O or name CB )) or resid 23 through 26 or (resid 27 and (nam \ e N or name CA or name C or name O or name CB )) or resid 28 through 31 or (resi \ d 32 and (name N or name CA or name C or name O or name CB )) or resid 33 or res \ id 47 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 and (name N or name CA or name C or n \ ame O or name CB )) or resid 69 through 73 or (resid 74 and (name N or name CA o \ r name C or name O or name CB )) or resid 75 through 103 or (resid 104 and (name \ N or name CA or name C or name O or name CB )) or resid 109 through 112 or (res \ id 113 and (name N or name CA or name C or name O or name CB )) or resid 114 thr \ ough 137 or (resid 138 through 141 and (name N or name CA or name C or name O or \ name CB )) or resid 142 through 160 or resid 162 through 167 or (resid 168 and \ (name N or name CA or name C or name O or name CB )) or resid 169 through 205 or \ (resid 206 and (name N or name CA or name C or name O or name CB )) or resid 20 \ 7 or (resid 208 and (name N or name CA or name C or name O or name CB or name OX \ T)))) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 8.320 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 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 : 0.003 0.079 8135 Z= 0.186 Angle : 0.596 9.186 11008 Z= 0.348 Chirality : 0.041 0.513 1335 Planarity : 0.004 0.048 1317 Dihedral : 13.897 80.356 2928 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 0.49 % Allowed : 0.25 % Favored : 99.26 % Cbeta Deviations : 0.10 % 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: 3.94 (0.26), residues: 979 helix: 3.25 (0.17), residues: 749 sheet: None (None), residues: 0 loop : 0.31 (0.41), residues: 230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 169 TYR 0.010 0.001 TYR A 82 PHE 0.020 0.001 PHE C 163 TRP 0.011 0.001 TRP C 100 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 8135) covalent geometry : angle 0.59604 (11008) hydrogen bonds : bond 0.10717 ( 636) hydrogen bonds : angle 4.21784 ( 1878) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 227 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: E 29 ILE cc_start: 0.7568 (mm) cc_final: 0.7275 (mm) REVERT: E 196 PHE cc_start: 0.8885 (t80) cc_final: 0.8608 (t80) REVERT: D 51 ASP cc_start: 0.8433 (t0) cc_final: 0.8196 (t0) REVERT: D 157 ARG cc_start: 0.7167 (OUTLIER) cc_final: 0.6941 (ttm110) REVERT: B 51 ASP cc_start: 0.8534 (t0) cc_final: 0.8095 (t0) REVERT: B 78 TYR cc_start: 0.8406 (t80) cc_final: 0.8082 (t80) REVERT: B 157 ARG cc_start: 0.6843 (OUTLIER) cc_final: 0.6629 (ttp-110) REVERT: A 83 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7929 (tm-30) REVERT: A 101 LYS cc_start: 0.7448 (tptt) cc_final: 0.7091 (tptt) outliers start: 3 outliers final: 0 residues processed: 230 average time/residue: 0.0877 time to fit residues: 27.0073 Evaluate side-chains 178 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 176 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 ARG Chi-restraints excluded: chain B residue 157 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 51 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.191105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.146962 restraints weight = 8295.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148995 restraints weight = 6771.729| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.150054 restraints weight = 5946.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150838 restraints weight = 5482.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.150887 restraints weight = 5169.421| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3675 r_free = 0.3675 target_work(ls_wunit_k1) = 0.148 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8135 Z= 0.129 Angle : 0.520 9.378 11008 Z= 0.262 Chirality : 0.038 0.168 1335 Planarity : 0.003 0.031 1317 Dihedral : 3.929 43.446 1089 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.84 % Allowed : 10.26 % Favored : 86.90 % 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: 4.27 (0.25), residues: 979 helix: 3.49 (0.17), residues: 751 sheet: None (None), residues: 0 loop : 0.38 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 99 TYR 0.018 0.001 TYR A 87 PHE 0.030 0.001 PHE C 49 TRP 0.016 0.001 TRP A 202 HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 8135) covalent geometry : angle 0.51965 (11008) hydrogen bonds : bond 0.04443 ( 636) hydrogen bonds : angle 3.36928 ( 1878) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 190 time to evaluate : 0.318 Fit side-chains REVERT: E 29 ILE cc_start: 0.7740 (mm) cc_final: 0.7407 (mm) REVERT: E 196 PHE cc_start: 0.8886 (t80) cc_final: 0.8582 (t80) REVERT: D 51 ASP cc_start: 0.8641 (t0) cc_final: 0.8359 (t0) REVERT: D 82 TYR cc_start: 0.8841 (t80) cc_final: 0.7767 (t80) REVERT: D 168 GLU cc_start: 0.7731 (tm-30) cc_final: 0.7407 (tp30) REVERT: C 102 GLN cc_start: 0.6919 (mm-40) cc_final: 0.6622 (mt0) REVERT: A 83 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7991 (tm-30) REVERT: A 101 LYS cc_start: 0.7421 (tptt) cc_final: 0.7135 (tptt) outliers start: 22 outliers final: 15 residues processed: 204 average time/residue: 0.0907 time to fit residues: 25.1110 Evaluate side-chains 185 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 170 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain D residue 71 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 190 ILE Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 78 optimal weight: 0.8980 chunk 3 optimal weight: 20.0000 chunk 30 optimal weight: 0.0570 chunk 45 optimal weight: 1.9990 chunk 44 optimal weight: 0.0980 chunk 41 optimal weight: 0.7980 chunk 21 optimal weight: 5.9990 chunk 53 optimal weight: 0.0670 chunk 24 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 6 optimal weight: 0.9990 overall best weight: 0.3836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.196100 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.155985 restraints weight = 6777.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.157439 restraints weight = 5904.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 19)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.157797 restraints weight = 5377.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.158513 restraints weight = 5163.218| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.158905 restraints weight = 4904.006| |-----------------------------------------------------------------------------| r_work (final): 0.3774 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3775 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3775 r_free = 0.3775 target_work(ls_wunit_k1) = 0.156 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8135 Z= 0.108 Angle : 0.483 8.395 11008 Z= 0.240 Chirality : 0.037 0.178 1335 Planarity : 0.003 0.033 1317 Dihedral : 3.172 15.373 1081 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.72 % Allowed : 13.10 % Favored : 84.18 % 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: 4.43 (0.25), residues: 979 helix: 3.62 (0.17), residues: 751 sheet: None (None), residues: 0 loop : 0.36 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 31 TYR 0.012 0.001 TYR E 87 PHE 0.030 0.001 PHE C 49 TRP 0.012 0.001 TRP A 202 HIS 0.004 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00227 ( 8135) covalent geometry : angle 0.48317 (11008) hydrogen bonds : bond 0.03633 ( 636) hydrogen bonds : angle 3.12032 ( 1878) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 188 time to evaluate : 0.236 Fit side-chains revert: symmetry clash REVERT: E 29 ILE cc_start: 0.7672 (mm) cc_final: 0.7379 (mm) REVERT: E 98 GLU cc_start: 0.8856 (tt0) cc_final: 0.8634 (tt0) REVERT: E 173 GLU cc_start: 0.6252 (tt0) cc_final: 0.5998 (tt0) REVERT: E 196 PHE cc_start: 0.8899 (t80) cc_final: 0.8591 (t80) REVERT: D 51 ASP cc_start: 0.8670 (t0) cc_final: 0.8309 (t0) REVERT: D 82 TYR cc_start: 0.8852 (t80) cc_final: 0.7977 (t80) REVERT: D 98 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8395 (mt-10) REVERT: D 137 LEU cc_start: 0.9025 (tp) cc_final: 0.8728 (mp) REVERT: D 205 MET cc_start: 0.8440 (mmp) cc_final: 0.8213 (mmp) REVERT: C 102 GLN cc_start: 0.6968 (mm-40) cc_final: 0.6663 (mt0) REVERT: A 83 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7900 (tm-30) REVERT: A 98 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7521 (mm-30) REVERT: A 101 LYS cc_start: 0.7315 (tptt) cc_final: 0.7030 (tptt) outliers start: 21 outliers final: 13 residues processed: 201 average time/residue: 0.0809 time to fit residues: 22.2721 Evaluate side-chains 185 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 171 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain D residue 50 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 13 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 17 optimal weight: 6.9990 chunk 79 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 73 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.186126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.141990 restraints weight = 6901.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.143482 restraints weight = 6035.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144244 restraints weight = 5522.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144244 restraints weight = 5202.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144244 restraints weight = 5202.788| |-----------------------------------------------------------------------------| r_work (final): 0.3609 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3610 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3610 r_free = 0.3610 target_work(ls_wunit_k1) = 0.142 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3610 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 8135 Z= 0.159 Angle : 0.542 9.508 11008 Z= 0.267 Chirality : 0.038 0.170 1335 Planarity : 0.003 0.033 1317 Dihedral : 3.316 15.558 1081 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Rotamer: Outliers : 3.46 % Allowed : 14.96 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 4.06 (0.25), residues: 979 helix: 3.39 (0.17), residues: 751 sheet: None (None), residues: 0 loop : 0.12 (0.41), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 99 TYR 0.013 0.001 TYR A 87 PHE 0.022 0.002 PHE D 196 TRP 0.014 0.001 TRP D 202 HIS 0.005 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 8135) covalent geometry : angle 0.54172 (11008) hydrogen bonds : bond 0.04882 ( 636) hydrogen bonds : angle 3.31535 ( 1878) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 175 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 20 THR cc_start: 0.9002 (p) cc_final: 0.8787 (t) REVERT: E 29 ILE cc_start: 0.7596 (mm) cc_final: 0.7362 (mm) REVERT: E 98 GLU cc_start: 0.8933 (tt0) cc_final: 0.8709 (tt0) REVERT: E 196 PHE cc_start: 0.8934 (t80) cc_final: 0.8622 (t80) REVERT: D 51 ASP cc_start: 0.8712 (t0) cc_final: 0.8369 (t0) REVERT: C 102 GLN cc_start: 0.7037 (mm-40) cc_final: 0.6817 (tt0) REVERT: A 83 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7866 (tm-30) REVERT: A 89 GLN cc_start: 0.4873 (mt0) cc_final: 0.4660 (mt0) outliers start: 27 outliers final: 24 residues processed: 195 average time/residue: 0.0800 time to fit residues: 21.6261 Evaluate side-chains 193 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 169 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 133 ILE Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 190 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 167 ILE Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 17 SER Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 42 optimal weight: 7.9990 chunk 84 optimal weight: 3.9990 chunk 29 optimal weight: 0.2980 chunk 71 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 47 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.189431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.142170 restraints weight = 12007.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.145344 restraints weight = 8531.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.147430 restraints weight = 6811.342| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.148506 restraints weight = 5957.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149358 restraints weight = 5471.233| |-----------------------------------------------------------------------------| r_work (final): 0.3668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3667 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3667 r_free = 0.3667 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3667 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.2460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 8135 Z= 0.115 Angle : 0.492 9.147 11008 Z= 0.242 Chirality : 0.037 0.170 1335 Planarity : 0.003 0.033 1317 Dihedral : 3.164 15.242 1081 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.82 % Favored : 99.18 % Rotamer: Outliers : 2.97 % Allowed : 16.32 % Favored : 80.72 % 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: 4.28 (0.25), residues: 979 helix: 3.58 (0.17), residues: 751 sheet: None (None), residues: 0 loop : 0.06 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 99 TYR 0.009 0.001 TYR E 87 PHE 0.023 0.001 PHE C 49 TRP 0.015 0.001 TRP B 202 HIS 0.005 0.000 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8135) covalent geometry : angle 0.49207 (11008) hydrogen bonds : bond 0.03979 ( 636) hydrogen bonds : angle 3.07890 ( 1878) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 178 time to evaluate : 0.297 Fit side-chains revert: symmetry clash REVERT: E 29 ILE cc_start: 0.7673 (mm) cc_final: 0.7449 (mm) REVERT: E 84 GLU cc_start: 0.8022 (mm-30) cc_final: 0.7810 (mm-30) REVERT: E 196 PHE cc_start: 0.8914 (t80) cc_final: 0.8461 (t80) REVERT: D 51 ASP cc_start: 0.8685 (t0) cc_final: 0.8329 (t0) REVERT: A 83 GLU cc_start: 0.8431 (mm-30) cc_final: 0.7865 (tm-30) REVERT: A 98 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7554 (mm-30) outliers start: 23 outliers final: 17 residues processed: 193 average time/residue: 0.0752 time to fit residues: 20.1890 Evaluate side-chains 191 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 68 optimal weight: 0.9990 chunk 44 optimal weight: 1.9990 chunk 94 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 81 optimal weight: 40.0000 chunk 69 optimal weight: 0.5980 chunk 97 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN A 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4025 r_free = 0.4025 target = 0.187574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.142874 restraints weight = 8554.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.144597 restraints weight = 6945.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145796 restraints weight = 6086.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.146995 restraints weight = 5583.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.147294 restraints weight = 5288.571| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.46 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3655 r_free = 0.3655 target_work(ls_wunit_k1) = 0.146 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.2659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8135 Z= 0.130 Angle : 0.535 13.609 11008 Z= 0.258 Chirality : 0.037 0.164 1335 Planarity : 0.003 0.032 1317 Dihedral : 3.186 15.335 1081 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 3.09 % Allowed : 16.69 % Favored : 80.22 % 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: 4.22 (0.25), residues: 979 helix: 3.54 (0.17), residues: 751 sheet: None (None), residues: 0 loop : 0.00 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 99 TYR 0.011 0.001 TYR C 78 PHE 0.029 0.001 PHE D 196 TRP 0.016 0.001 TRP B 202 HIS 0.009 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 8135) covalent geometry : angle 0.53477 (11008) hydrogen bonds : bond 0.04172 ( 636) hydrogen bonds : angle 3.13406 ( 1878) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 182 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: E 29 ILE cc_start: 0.7718 (mm) cc_final: 0.7493 (mm) REVERT: E 87 TYR cc_start: 0.7891 (t80) cc_final: 0.7595 (t80) REVERT: D 51 ASP cc_start: 0.8674 (t0) cc_final: 0.8291 (t0) REVERT: C 46 GLN cc_start: 0.7042 (mm110) cc_final: 0.6598 (mm-40) REVERT: A 83 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7835 (tm-30) REVERT: A 98 GLU cc_start: 0.7849 (OUTLIER) cc_final: 0.7479 (mm-30) outliers start: 24 outliers final: 21 residues processed: 198 average time/residue: 0.0745 time to fit residues: 20.0905 Evaluate side-chains 195 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 0.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 98 GLU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 64 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 4.9990 chunk 55 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 84 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.187409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.142941 restraints weight = 8250.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.144909 restraints weight = 6808.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145931 restraints weight = 6004.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146297 restraints weight = 5529.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.147200 restraints weight = 5324.234| |-----------------------------------------------------------------------------| r_work (final): 0.3673 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3674 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3674 r_free = 0.3674 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3674 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8135 Z= 0.135 Angle : 0.549 13.103 11008 Z= 0.264 Chirality : 0.037 0.162 1335 Planarity : 0.003 0.031 1317 Dihedral : 3.194 15.174 1081 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 3.21 % Allowed : 18.05 % Favored : 78.74 % 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: 4.19 (0.26), residues: 979 helix: 3.54 (0.17), residues: 751 sheet: None (None), residues: 0 loop : -0.05 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 99 TYR 0.008 0.001 TYR C 78 PHE 0.033 0.001 PHE D 196 TRP 0.019 0.001 TRP B 202 HIS 0.008 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 8135) covalent geometry : angle 0.54909 (11008) hydrogen bonds : bond 0.04254 ( 636) hydrogen bonds : angle 3.17180 ( 1878) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 174 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: E 22 THR cc_start: 0.9062 (t) cc_final: 0.8718 (p) REVERT: E 29 ILE cc_start: 0.7718 (mm) cc_final: 0.7507 (mm) REVERT: D 51 ASP cc_start: 0.8666 (t0) cc_final: 0.8313 (t0) REVERT: C 80 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8499 (tt) REVERT: B 31 ARG cc_start: 0.8495 (mtm180) cc_final: 0.8223 (mtm180) REVERT: A 83 GLU cc_start: 0.8264 (mm-30) cc_final: 0.7737 (tm-30) REVERT: A 98 GLU cc_start: 0.7967 (tp30) cc_final: 0.7628 (mm-30) outliers start: 25 outliers final: 23 residues processed: 190 average time/residue: 0.0780 time to fit residues: 20.6298 Evaluate side-chains 190 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 133 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 84 GLU Chi-restraints excluded: chain A residue 133 ILE Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 81 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 2 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 26 optimal weight: 0.4980 chunk 57 optimal weight: 0.6980 chunk 39 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.191619 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.147898 restraints weight = 8128.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.149794 restraints weight = 6658.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150641 restraints weight = 5830.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150641 restraints weight = 5411.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.150641 restraints weight = 5411.817| |-----------------------------------------------------------------------------| r_work (final): 0.3688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.149 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7617 moved from start: 0.2931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8135 Z= 0.112 Angle : 0.535 11.982 11008 Z= 0.255 Chirality : 0.037 0.162 1335 Planarity : 0.003 0.032 1317 Dihedral : 3.091 15.083 1081 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.60 % Allowed : 19.28 % Favored : 78.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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 (0.26), residues: 979 helix: 3.69 (0.17), residues: 750 sheet: 1.58 (1.63), residues: 10 loop : -0.01 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.008 0.001 TYR C 78 PHE 0.034 0.001 PHE D 196 TRP 0.019 0.001 TRP D 202 HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 8135) covalent geometry : angle 0.53453 (11008) hydrogen bonds : bond 0.03545 ( 636) hydrogen bonds : angle 3.03970 ( 1878) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 175 time to evaluate : 0.305 Fit side-chains REVERT: E 22 THR cc_start: 0.9106 (t) cc_final: 0.8766 (p) REVERT: E 29 ILE cc_start: 0.7749 (mm) cc_final: 0.7510 (mm) REVERT: D 51 ASP cc_start: 0.8653 (t0) cc_final: 0.8243 (t0) REVERT: B 31 ARG cc_start: 0.8513 (mtm180) cc_final: 0.8289 (mtm180) outliers start: 20 outliers final: 17 residues processed: 190 average time/residue: 0.0801 time to fit residues: 21.0605 Evaluate side-chains 190 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 173 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 0 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 63 optimal weight: 0.0020 chunk 62 optimal weight: 0.9980 chunk 91 optimal weight: 5.9990 chunk 33 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 0.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.191475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.149034 restraints weight = 6756.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.150166 restraints weight = 5884.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151352 restraints weight = 5379.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151352 restraints weight = 5044.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.151352 restraints weight = 5044.495| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3699 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3699 r_free = 0.3699 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3699 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7613 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8135 Z= 0.117 Angle : 0.554 12.011 11008 Z= 0.266 Chirality : 0.037 0.159 1335 Planarity : 0.003 0.033 1317 Dihedral : 3.101 15.453 1081 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % Rotamer: Outliers : 2.84 % Allowed : 18.91 % Favored : 78.24 % 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: 4.38 (0.26), residues: 979 helix: 3.65 (0.17), residues: 750 sheet: 1.55 (1.66), residues: 10 loop : 0.04 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.013 0.001 TYR C 78 PHE 0.035 0.001 PHE D 196 TRP 0.020 0.001 TRP D 202 HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 8135) covalent geometry : angle 0.55379 (11008) hydrogen bonds : bond 0.03610 ( 636) hydrogen bonds : angle 3.06892 ( 1878) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 171 time to evaluate : 0.329 Fit side-chains revert: symmetry clash REVERT: E 22 THR cc_start: 0.9123 (t) cc_final: 0.8824 (p) REVERT: E 29 ILE cc_start: 0.7752 (mm) cc_final: 0.7538 (mm) REVERT: E 196 PHE cc_start: 0.8963 (t80) cc_final: 0.8699 (t80) REVERT: D 51 ASP cc_start: 0.8700 (t0) cc_final: 0.8315 (t0) REVERT: C 80 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8492 (tt) REVERT: B 31 ARG cc_start: 0.8577 (mtm180) cc_final: 0.8348 (mtm180) REVERT: B 96 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7702 (mp0) outliers start: 22 outliers final: 19 residues processed: 189 average time/residue: 0.0773 time to fit residues: 20.4167 Evaluate side-chains 188 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 168 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 50 optimal weight: 0.8980 chunk 29 optimal weight: 4.9990 chunk 23 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 95 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 33 optimal weight: 10.0000 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4018 r_free = 0.4018 target = 0.186907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.143775 restraints weight = 6701.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.144956 restraints weight = 5971.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.145367 restraints weight = 5512.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145785 restraints weight = 5295.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.145785 restraints weight = 5168.270| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3639 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3639 r_free = 0.3639 target_work(ls_wunit_k1) = 0.144 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3639 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.3063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8135 Z= 0.147 Angle : 0.585 12.657 11008 Z= 0.284 Chirality : 0.038 0.160 1335 Planarity : 0.003 0.034 1317 Dihedral : 3.208 15.511 1081 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.72 % Allowed : 19.65 % Favored : 77.63 % 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: 4.18 (0.25), residues: 979 helix: 3.51 (0.17), residues: 750 sheet: 1.26 (1.73), residues: 10 loop : -0.04 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.009 0.001 TYR A 78 PHE 0.033 0.001 PHE D 196 TRP 0.022 0.001 TRP D 202 HIS 0.006 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00354 ( 8135) covalent geometry : angle 0.58468 (11008) hydrogen bonds : bond 0.04328 ( 636) hydrogen bonds : angle 3.21403 ( 1878) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1958 Ramachandran restraints generated. 979 Oldfield, 0 Emsley, 979 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 169 time to evaluate : 0.185 Fit side-chains revert: symmetry clash REVERT: E 22 THR cc_start: 0.9085 (t) cc_final: 0.8773 (p) REVERT: E 29 ILE cc_start: 0.7765 (mm) cc_final: 0.7563 (mm) REVERT: D 51 ASP cc_start: 0.8682 (t0) cc_final: 0.8342 (t0) REVERT: C 80 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8537 (tt) REVERT: B 31 ARG cc_start: 0.8541 (mtm180) cc_final: 0.8268 (mtm180) REVERT: B 96 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7743 (mp0) outliers start: 21 outliers final: 20 residues processed: 185 average time/residue: 0.0713 time to fit residues: 18.7769 Evaluate side-chains 189 residues out of total 870 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 168 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 91 GLN Chi-restraints excluded: chain E residue 126 VAL Chi-restraints excluded: chain E residue 163 PHE Chi-restraints excluded: chain E residue 167 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 198 ILE Chi-restraints excluded: chain C residue 16 SER Chi-restraints excluded: chain C residue 40 VAL Chi-restraints excluded: chain C residue 80 LEU Chi-restraints excluded: chain C residue 128 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 192 LEU Chi-restraints excluded: chain B residue 29 ILE Chi-restraints excluded: chain B residue 65 ARG Chi-restraints excluded: chain B residue 97 MET Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 134 LEU Chi-restraints excluded: chain A residue 190 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 90 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 58 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 4.9990 chunk 2 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.187880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.144373 restraints weight = 6944.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.145601 restraints weight = 6096.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 17)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.146219 restraints weight = 5575.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.147034 restraints weight = 5288.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.147792 restraints weight = 5015.464| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.147 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.3113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 8135 Z= 0.137 Angle : 0.577 12.319 11008 Z= 0.280 Chirality : 0.038 0.161 1335 Planarity : 0.003 0.034 1317 Dihedral : 3.194 15.292 1081 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.60 % Allowed : 20.15 % Favored : 77.26 % 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: 4.19 (0.25), residues: 979 helix: 3.53 (0.17), residues: 751 sheet: None (None), residues: 0 loop : -0.05 (0.39), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 99 TYR 0.009 0.001 TYR C 78 PHE 0.032 0.001 PHE D 196 TRP 0.022 0.001 TRP D 202 HIS 0.007 0.001 HIS C 47 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8135) covalent geometry : angle 0.57687 (11008) hydrogen bonds : bond 0.04196 ( 636) hydrogen bonds : angle 3.19177 ( 1878) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1321.40 seconds wall clock time: 23 minutes 23.84 seconds (1403.84 seconds total)