Starting phenix.real_space_refine on Fri Mar 15 21:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8d66_27218/03_2024/8d66_27218_neut_updated.pdb" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 5 5.49 5 S 35 5.16 5 C 8375 2.51 5 N 2085 2.21 5 O 2300 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 150": "OE1" <-> "OE2" Residue "A GLU 155": "OE1" <-> "OE2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A GLU 230": "OE1" <-> "OE2" Residue "A ARG 286": "NH1" <-> "NH2" Residue "B GLU 131": "OE1" <-> "OE2" Residue "B GLU 150": "OE1" <-> "OE2" Residue "B GLU 155": "OE1" <-> "OE2" Residue "B GLU 226": "OE1" <-> "OE2" Residue "B GLU 230": "OE1" <-> "OE2" Residue "B ARG 286": "NH1" <-> "NH2" Residue "C GLU 131": "OE1" <-> "OE2" Residue "C GLU 150": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C GLU 226": "OE1" <-> "OE2" Residue "C GLU 230": "OE1" <-> "OE2" Residue "C ARG 286": "NH1" <-> "NH2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 150": "OE1" <-> "OE2" Residue "D GLU 155": "OE1" <-> "OE2" Residue "D GLU 226": "OE1" <-> "OE2" Residue "D GLU 230": "OE1" <-> "OE2" Residue "D ARG 286": "NH1" <-> "NH2" Residue "E GLU 131": "OE1" <-> "OE2" Residue "E GLU 150": "OE1" <-> "OE2" Residue "E GLU 155": "OE1" <-> "OE2" Residue "E GLU 226": "OE1" <-> "OE2" Residue "E GLU 230": "OE1" <-> "OE2" Residue "E ARG 286": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12800 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "B" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "C" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "D" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "E" Number of atoms: 2505 Number of conformers: 1 Conformer: "" Number of residues, atoms: 307, 2505 Classifications: {'peptide': 307} Link IDs: {'PTRANS': 14, 'TRANS': 292} Chain: "A" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 55 Unusual residues: {'DHL': 1, 'PGW': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 6.74, per 1000 atoms: 0.53 Number of scatterers: 12800 At special positions: 0 Unit cell: (90.2, 90.2, 125.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 35 16.00 P 5 15.00 O 2300 8.00 N 2085 7.00 C 8375 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.79 Conformation dependent library (CDL) restraints added in 2.2 seconds 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2910 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 15 sheets defined 29.5% alpha, 26.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.06 Creating SS restraints... Processing helix chain 'A' and resid 63 through 69 removed outlier: 3.531A pdb=" N ASN A 69 " --> pdb=" O ARG A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 202 through 208 Processing helix chain 'A' and resid 210 through 224 removed outlier: 3.801A pdb=" N VAL A 222 " --> pdb=" O ALA A 218 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE A 223 " --> pdb=" O SER A 219 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP A 224 " --> pdb=" O TRP A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 248 Processing helix chain 'A' and resid 261 through 284 Processing helix chain 'A' and resid 303 through 316 removed outlier: 3.594A pdb=" N PHE A 308 " --> pdb=" O PHE A 304 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 69 removed outlier: 3.531A pdb=" N ASN B 69 " --> pdb=" O ARG B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 202 through 208 Processing helix chain 'B' and resid 210 through 224 removed outlier: 3.801A pdb=" N VAL B 222 " --> pdb=" O ALA B 218 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP B 224 " --> pdb=" O TRP B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 248 Processing helix chain 'B' and resid 261 through 284 Processing helix chain 'B' and resid 303 through 316 removed outlier: 3.593A pdb=" N PHE B 308 " --> pdb=" O PHE B 304 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 69 removed outlier: 3.531A pdb=" N ASN C 69 " --> pdb=" O ARG C 65 " (cutoff:3.500A) Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'C' and resid 210 through 224 removed outlier: 3.800A pdb=" N VAL C 222 " --> pdb=" O ALA C 218 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE C 223 " --> pdb=" O SER C 219 " (cutoff:3.500A) removed outlier: 5.472A pdb=" N TRP C 224 " --> pdb=" O TRP C 220 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 248 Processing helix chain 'C' and resid 261 through 284 Processing helix chain 'C' and resid 303 through 316 removed outlier: 3.594A pdb=" N PHE C 308 " --> pdb=" O PHE C 304 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 69 removed outlier: 3.531A pdb=" N ASN D 69 " --> pdb=" O ARG D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 202 through 208 Processing helix chain 'D' and resid 210 through 224 removed outlier: 3.801A pdb=" N VAL D 222 " --> pdb=" O ALA D 218 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP D 224 " --> pdb=" O TRP D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 248 Processing helix chain 'D' and resid 261 through 284 Processing helix chain 'D' and resid 303 through 316 removed outlier: 3.593A pdb=" N PHE D 308 " --> pdb=" O PHE D 304 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 69 removed outlier: 3.531A pdb=" N ASN E 69 " --> pdb=" O ARG E 65 " (cutoff:3.500A) Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 202 through 208 Processing helix chain 'E' and resid 210 through 224 removed outlier: 3.800A pdb=" N VAL E 222 " --> pdb=" O ALA E 218 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N PHE E 223 " --> pdb=" O SER E 219 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N TRP E 224 " --> pdb=" O TRP E 220 " (cutoff:3.500A) Processing helix chain 'E' and resid 228 through 248 Processing helix chain 'E' and resid 261 through 284 Processing helix chain 'E' and resid 303 through 316 removed outlier: 3.594A pdb=" N PHE E 308 " --> pdb=" O PHE E 304 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 12 through 14 Processing sheet with id= B, first strand: chain 'A' and resid 145 through 147 removed outlier: 6.939A pdb=" N VAL A 16 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP A 36 " --> pdb=" O ASN A 21 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE A 23 " --> pdb=" O LYS A 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS A 34 " --> pdb=" O ILE A 23 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER A 189 " --> pdb=" O PRO A 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP A 196 " --> pdb=" O LYS A 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS A 165 " --> pdb=" O ASP A 196 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL A 198 " --> pdb=" O ARG A 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG A 163 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 12 through 14 Processing sheet with id= E, first strand: chain 'B' and resid 145 through 147 removed outlier: 6.939A pdb=" N VAL B 16 " --> pdb=" O GLN B 146 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP B 36 " --> pdb=" O ASN B 21 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE B 23 " --> pdb=" O LYS B 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS B 34 " --> pdb=" O ILE B 23 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER B 189 " --> pdb=" O PRO B 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP B 196 " --> pdb=" O LYS B 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS B 165 " --> pdb=" O ASP B 196 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N VAL B 198 " --> pdb=" O ARG B 163 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ARG B 163 " --> pdb=" O VAL B 198 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 12 through 14 Processing sheet with id= H, first strand: chain 'C' and resid 145 through 147 removed outlier: 6.938A pdb=" N VAL C 16 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP C 36 " --> pdb=" O ASN C 21 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ILE C 23 " --> pdb=" O LYS C 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS C 34 " --> pdb=" O ILE C 23 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER C 189 " --> pdb=" O PRO C 132 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP C 196 " --> pdb=" O LYS C 165 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS C 165 " --> pdb=" O ASP C 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL C 198 " --> pdb=" O ARG C 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG C 163 " --> pdb=" O VAL C 198 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 12 through 14 Processing sheet with id= K, first strand: chain 'D' and resid 145 through 147 removed outlier: 6.939A pdb=" N VAL D 16 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ASP D 36 " --> pdb=" O ASN D 21 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE D 23 " --> pdb=" O LYS D 34 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LYS D 34 " --> pdb=" O ILE D 23 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER D 189 " --> pdb=" O PRO D 132 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP D 196 " --> pdb=" O LYS D 165 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LYS D 165 " --> pdb=" O ASP D 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL D 198 " --> pdb=" O ARG D 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG D 163 " --> pdb=" O VAL D 198 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 12 through 14 Processing sheet with id= N, first strand: chain 'E' and resid 145 through 147 removed outlier: 6.939A pdb=" N VAL E 16 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ASP E 36 " --> pdb=" O ASN E 21 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N ILE E 23 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N LYS E 34 " --> pdb=" O ILE E 23 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.712A pdb=" N SER E 189 " --> pdb=" O PRO E 132 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASP E 196 " --> pdb=" O LYS E 165 " (cutoff:3.500A) removed outlier: 7.187A pdb=" N LYS E 165 " --> pdb=" O ASP E 196 " (cutoff:3.500A) removed outlier: 7.325A pdb=" N VAL E 198 " --> pdb=" O ARG E 163 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARG E 163 " --> pdb=" O VAL E 198 " (cutoff:3.500A) 520 hydrogen bonds defined for protein. 1545 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: 3.41 Time building geometry restraints manager: 5.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 2021 1.31 - 1.43: 3759 1.43 - 1.56: 7285 1.56 - 1.68: 10 1.68 - 1.81: 55 Bond restraints: 13130 Sorted by residual: bond pdb=" C1 PGW C 401 " pdb=" O01 PGW C 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" C1 PGW A 401 " pdb=" O01 PGW A 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 PGW D 401 " pdb=" O01 PGW D 401 " ideal model delta sigma weight residual 1.332 1.402 -0.070 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C1 PGW E 401 " pdb=" O01 PGW E 401 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.21e+01 bond pdb=" C19 PGW A 401 " pdb=" O03 PGW A 401 " ideal model delta sigma weight residual 1.332 1.401 -0.069 2.00e-02 2.50e+03 1.20e+01 ... (remaining 13125 not shown) Histogram of bond angle deviations from ideal: 100.24 - 107.08: 416 107.08 - 113.92: 7339 113.92 - 120.77: 5740 120.77 - 127.61: 4173 127.61 - 134.46: 157 Bond angle restraints: 17825 Sorted by residual: angle pdb=" O11 PGW C 401 " pdb=" P PGW C 401 " pdb=" O12 PGW C 401 " ideal model delta sigma weight residual 98.90 110.62 -11.72 3.00e+00 1.11e-01 1.53e+01 angle pdb=" O11 PGW A 401 " pdb=" P PGW A 401 " pdb=" O12 PGW A 401 " ideal model delta sigma weight residual 98.90 110.59 -11.69 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW B 401 " pdb=" P PGW B 401 " pdb=" O12 PGW B 401 " ideal model delta sigma weight residual 98.90 110.58 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW E 401 " pdb=" P PGW E 401 " pdb=" O12 PGW E 401 " ideal model delta sigma weight residual 98.90 110.58 -11.68 3.00e+00 1.11e-01 1.52e+01 angle pdb=" O11 PGW D 401 " pdb=" P PGW D 401 " pdb=" O12 PGW D 401 " ideal model delta sigma weight residual 98.90 110.56 -11.66 3.00e+00 1.11e-01 1.51e+01 ... (remaining 17820 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.71: 7531 34.71 - 69.42: 184 69.42 - 104.12: 20 104.12 - 138.83: 25 138.83 - 173.54: 5 Dihedral angle restraints: 7765 sinusoidal: 3260 harmonic: 4505 Sorted by residual: dihedral pdb=" CA LEU B 118 " pdb=" C LEU B 118 " pdb=" N PHE B 119 " pdb=" CA PHE B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.11 -25.89 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU E 118 " pdb=" C LEU E 118 " pdb=" N PHE E 119 " pdb=" CA PHE E 119 " ideal model delta harmonic sigma weight residual -180.00 -154.12 -25.88 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA LEU C 118 " pdb=" C LEU C 118 " pdb=" N PHE C 119 " pdb=" CA PHE C 119 " ideal model delta harmonic sigma weight residual -180.00 -154.14 -25.86 0 5.00e+00 4.00e-02 2.68e+01 ... (remaining 7762 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 1385 0.057 - 0.115: 438 0.115 - 0.172: 107 0.172 - 0.230: 25 0.230 - 0.287: 5 Chirality restraints: 1960 Sorted by residual: chirality pdb=" CA THR C 61 " pdb=" N THR C 61 " pdb=" C THR C 61 " pdb=" CB THR C 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA THR B 61 " pdb=" N THR B 61 " pdb=" C THR B 61 " pdb=" CB THR B 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CA THR E 61 " pdb=" N THR E 61 " pdb=" C THR E 61 " pdb=" CB THR E 61 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.04e+00 ... (remaining 1957 not shown) Planarity restraints: 2250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP D 206 " 0.021 2.00e-02 2.50e+03 1.65e-02 6.80e+00 pdb=" CG TRP D 206 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP D 206 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP D 206 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP D 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP D 206 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP D 206 " -0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 206 " -0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 206 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP D 206 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 206 " -0.021 2.00e-02 2.50e+03 1.65e-02 6.78e+00 pdb=" CG TRP A 206 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP A 206 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP A 206 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP A 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP A 206 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 206 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 206 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP A 206 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 206 " -0.021 2.00e-02 2.50e+03 1.64e-02 6.70e+00 pdb=" CG TRP E 206 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP E 206 " -0.020 2.00e-02 2.50e+03 pdb=" CD2 TRP E 206 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP E 206 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP E 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP E 206 " 0.013 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 206 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 206 " -0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP E 206 " -0.011 2.00e-02 2.50e+03 ... (remaining 2247 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3876 2.83 - 3.35: 10848 3.35 - 3.86: 20332 3.86 - 4.38: 24465 4.38 - 4.90: 42848 Nonbonded interactions: 102369 Sorted by model distance: nonbonded pdb=" O SER D 221 " pdb=" OG SER D 221 " model vdw 2.309 2.440 nonbonded pdb=" O SER C 221 " pdb=" OG SER C 221 " model vdw 2.309 2.440 nonbonded pdb=" O SER E 221 " pdb=" OG SER E 221 " model vdw 2.309 2.440 nonbonded pdb=" O SER A 221 " pdb=" OG SER A 221 " model vdw 2.309 2.440 nonbonded pdb=" O SER B 221 " pdb=" OG SER B 221 " model vdw 2.309 2.440 ... (remaining 102364 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.440 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: 2.110 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 35.220 Find NCS groups from input model: 0.860 Set up NCS constraints: 0.080 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 : 0.009 0.070 13130 Z= 0.575 Angle : 1.018 11.720 17825 Z= 0.512 Chirality : 0.061 0.287 1960 Planarity : 0.005 0.039 2250 Dihedral : 18.545 173.540 4855 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.21), residues: 1525 helix: -0.19 (0.22), residues: 515 sheet: 0.28 (0.28), residues: 395 loop : -2.85 (0.21), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP C 206 HIS 0.004 0.002 HIS A 177 PHE 0.016 0.002 PHE D 228 TYR 0.023 0.003 TYR D 245 ARG 0.007 0.001 ARG B 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 159 time to evaluate : 1.334 Fit side-chains revert: symmetry clash REVERT: A 54 LYS cc_start: 0.8835 (mttt) cc_final: 0.8462 (mtmt) REVERT: A 86 ASP cc_start: 0.7856 (t0) cc_final: 0.7374 (t70) REVERT: A 174 ARG cc_start: 0.7609 (ttm-80) cc_final: 0.7352 (ttt-90) REVERT: B 54 LYS cc_start: 0.8558 (mttt) cc_final: 0.8270 (mtmt) REVERT: B 65 ARG cc_start: 0.7628 (mtp-110) cc_final: 0.7151 (mtm180) REVERT: B 86 ASP cc_start: 0.7812 (t0) cc_final: 0.7449 (t70) REVERT: B 90 LYS cc_start: 0.8884 (pttt) cc_final: 0.8651 (ptpp) REVERT: C 114 MET cc_start: 0.9024 (mtt) cc_final: 0.8761 (mtt) REVERT: C 265 MET cc_start: 0.8348 (mtp) cc_final: 0.8076 (mtp) REVERT: D 86 ASP cc_start: 0.7720 (t0) cc_final: 0.7269 (t70) REVERT: D 113 ASP cc_start: 0.7273 (m-30) cc_final: 0.7059 (p0) REVERT: E 21 ASN cc_start: 0.8540 (t0) cc_final: 0.8186 (t0) REVERT: E 54 LYS cc_start: 0.8752 (mttt) cc_final: 0.8133 (mtpp) REVERT: E 86 ASP cc_start: 0.7912 (t0) cc_final: 0.7397 (t70) REVERT: E 113 ASP cc_start: 0.7200 (m-30) cc_final: 0.6796 (p0) REVERT: E 174 ARG cc_start: 0.7690 (ttm-80) cc_final: 0.7351 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 159 average time/residue: 0.2786 time to fit residues: 61.6018 Evaluate side-chains 136 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 126 optimal weight: 0.9990 chunk 113 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 38 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 117 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 71 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 136 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN B 27 ASN C 27 ASN D 27 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13130 Z= 0.182 Angle : 0.534 5.249 17825 Z= 0.272 Chirality : 0.047 0.176 1960 Planarity : 0.004 0.036 2250 Dihedral : 14.818 92.213 1925 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.24 % Allowed : 5.60 % Favored : 93.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.22), residues: 1525 helix: 0.92 (0.24), residues: 515 sheet: 0.54 (0.28), residues: 395 loop : -2.55 (0.22), residues: 615 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 206 HIS 0.003 0.001 HIS A 177 PHE 0.012 0.001 PHE D 236 TYR 0.015 0.001 TYR C 245 ARG 0.002 0.000 ARG D 123 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 149 time to evaluate : 1.600 Fit side-chains REVERT: A 21 ASN cc_start: 0.8132 (t0) cc_final: 0.7927 (t0) REVERT: A 54 LYS cc_start: 0.8811 (mttt) cc_final: 0.8482 (mtmt) REVERT: A 86 ASP cc_start: 0.7813 (t0) cc_final: 0.7301 (t70) REVERT: A 155 GLU cc_start: 0.7892 (mm-30) cc_final: 0.7677 (mm-30) REVERT: A 156 GLU cc_start: 0.7187 (mp0) cc_final: 0.6804 (mp0) REVERT: A 174 ARG cc_start: 0.7691 (ttm-80) cc_final: 0.7338 (mtp85) REVERT: A 245 TYR cc_start: 0.7594 (m-80) cc_final: 0.7032 (m-80) REVERT: B 54 LYS cc_start: 0.8456 (mttt) cc_final: 0.8230 (mtmt) REVERT: B 65 ARG cc_start: 0.7717 (mtp-110) cc_final: 0.7328 (mtm180) REVERT: B 86 ASP cc_start: 0.7696 (t0) cc_final: 0.7326 (t70) REVERT: C 114 MET cc_start: 0.8881 (mtt) cc_final: 0.8483 (mtt) REVERT: C 255 ARG cc_start: 0.7963 (ptp-170) cc_final: 0.7743 (ptp-170) REVERT: C 265 MET cc_start: 0.8202 (mtp) cc_final: 0.7784 (mtp) REVERT: D 86 ASP cc_start: 0.7681 (t0) cc_final: 0.7256 (t70) REVERT: D 113 ASP cc_start: 0.7287 (m-30) cc_final: 0.6992 (p0) REVERT: E 21 ASN cc_start: 0.8263 (t0) cc_final: 0.7992 (t0) REVERT: E 54 LYS cc_start: 0.8709 (mttt) cc_final: 0.8445 (mttp) REVERT: E 113 ASP cc_start: 0.7172 (m-30) cc_final: 0.6824 (p0) REVERT: E 114 MET cc_start: 0.9099 (mtt) cc_final: 0.8658 (mtt) outliers start: 17 outliers final: 13 residues processed: 157 average time/residue: 0.2777 time to fit residues: 61.7597 Evaluate side-chains 140 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 127 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 75 optimal weight: 0.0030 chunk 42 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 37 optimal weight: 0.0970 chunk 136 optimal weight: 0.9990 chunk 147 optimal weight: 2.9990 chunk 121 optimal weight: 4.9990 chunk 135 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 109 optimal weight: 5.9990 overall best weight: 1.0194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.1529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 13130 Z= 0.163 Angle : 0.489 5.167 17825 Z= 0.248 Chirality : 0.047 0.205 1960 Planarity : 0.003 0.031 2250 Dihedral : 12.485 85.364 1925 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 2.25 % Allowed : 7.42 % Favored : 90.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.22), residues: 1525 helix: 1.11 (0.24), residues: 525 sheet: 0.75 (0.28), residues: 395 loop : -2.19 (0.23), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 206 HIS 0.002 0.001 HIS A 177 PHE 0.011 0.001 PHE E 236 TYR 0.015 0.001 TYR D 245 ARG 0.004 0.000 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 146 time to evaluate : 1.457 Fit side-chains REVERT: A 54 LYS cc_start: 0.8706 (mttt) cc_final: 0.8431 (mtmt) REVERT: A 156 GLU cc_start: 0.7074 (mp0) cc_final: 0.6730 (mp0) REVERT: A 174 ARG cc_start: 0.7716 (ttm-80) cc_final: 0.7437 (mtp85) REVERT: B 54 LYS cc_start: 0.8427 (mttt) cc_final: 0.8153 (mtmt) REVERT: B 65 ARG cc_start: 0.7712 (mtp-110) cc_final: 0.7345 (mtm180) REVERT: B 86 ASP cc_start: 0.7737 (t0) cc_final: 0.7363 (t70) REVERT: C 123 ARG cc_start: 0.7966 (ttt-90) cc_final: 0.7734 (ttt-90) REVERT: C 245 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.7532 (t80) REVERT: D 86 ASP cc_start: 0.7681 (t0) cc_final: 0.7228 (t70) REVERT: D 245 TYR cc_start: 0.7720 (OUTLIER) cc_final: 0.7478 (t80) REVERT: E 21 ASN cc_start: 0.8291 (t0) cc_final: 0.7997 (t0) REVERT: E 65 ARG cc_start: 0.7594 (mtp-110) cc_final: 0.7287 (mtm180) REVERT: E 156 GLU cc_start: 0.7149 (mp0) cc_final: 0.6740 (mp0) REVERT: E 245 TYR cc_start: 0.7644 (OUTLIER) cc_final: 0.6742 (t80) outliers start: 31 outliers final: 20 residues processed: 164 average time/residue: 0.2588 time to fit residues: 60.5635 Evaluate side-chains 149 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 126 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 245 TYR Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 0.0170 chunk 102 optimal weight: 5.9990 chunk 70 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 129 optimal weight: 5.9990 chunk 39 optimal weight: 0.6980 overall best weight: 0.9420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN C 27 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.1780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 13130 Z= 0.154 Angle : 0.480 5.109 17825 Z= 0.243 Chirality : 0.046 0.209 1960 Planarity : 0.003 0.031 2250 Dihedral : 11.506 78.554 1925 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.69 % Allowed : 8.95 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.23), residues: 1525 helix: 1.23 (0.24), residues: 530 sheet: 0.88 (0.28), residues: 395 loop : -2.22 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 206 HIS 0.002 0.001 HIS A 177 PHE 0.011 0.001 PHE E 236 TYR 0.014 0.001 TYR B 245 ARG 0.002 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 136 time to evaluate : 1.466 Fit side-chains REVERT: A 156 GLU cc_start: 0.7149 (mp0) cc_final: 0.6809 (mp0) REVERT: A 174 ARG cc_start: 0.7700 (ttm-80) cc_final: 0.7379 (ttt-90) REVERT: B 54 LYS cc_start: 0.8383 (mttt) cc_final: 0.8113 (mttp) REVERT: B 65 ARG cc_start: 0.7725 (mtp-110) cc_final: 0.7380 (mtm180) REVERT: B 86 ASP cc_start: 0.7832 (t0) cc_final: 0.7409 (t70) REVERT: B 123 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7587 (ttm-80) REVERT: C 30 GLU cc_start: 0.7004 (mt-10) cc_final: 0.6660 (tp30) REVERT: C 245 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7437 (t80) REVERT: C 252 ILE cc_start: 0.7903 (mm) cc_final: 0.7571 (pt) REVERT: C 255 ARG cc_start: 0.7742 (ptp-170) cc_final: 0.7379 (ptp-170) REVERT: D 86 ASP cc_start: 0.7719 (t0) cc_final: 0.7274 (t70) REVERT: E 65 ARG cc_start: 0.7576 (mtp-110) cc_final: 0.7288 (mtm180) REVERT: E 245 TYR cc_start: 0.7635 (OUTLIER) cc_final: 0.6774 (t80) outliers start: 37 outliers final: 28 residues processed: 162 average time/residue: 0.2599 time to fit residues: 59.9157 Evaluate side-chains 153 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 123 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 120 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 2 optimal weight: 4.9990 chunk 107 optimal weight: 0.9990 chunk 59 optimal weight: 9.9990 chunk 123 optimal weight: 0.9990 chunk 100 optimal weight: 0.0980 chunk 0 optimal weight: 6.9990 chunk 74 optimal weight: 3.9990 chunk 130 optimal weight: 0.2980 chunk 36 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN E 124 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 13130 Z= 0.147 Angle : 0.467 5.147 17825 Z= 0.236 Chirality : 0.046 0.211 1960 Planarity : 0.003 0.033 2250 Dihedral : 10.784 73.740 1925 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 2.69 % Allowed : 9.75 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1525 helix: 1.34 (0.24), residues: 530 sheet: 0.94 (0.28), residues: 395 loop : -2.17 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 206 HIS 0.002 0.000 HIS E 177 PHE 0.015 0.001 PHE B 236 TYR 0.014 0.001 TYR B 245 ARG 0.004 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 130 time to evaluate : 1.263 Fit side-chains REVERT: A 156 GLU cc_start: 0.6951 (mp0) cc_final: 0.6629 (mp0) REVERT: A 174 ARG cc_start: 0.7687 (ttm-80) cc_final: 0.7361 (ttt-90) REVERT: B 54 LYS cc_start: 0.8350 (mttt) cc_final: 0.8080 (mttp) REVERT: B 65 ARG cc_start: 0.7733 (mtp-110) cc_final: 0.7375 (mtm180) REVERT: B 86 ASP cc_start: 0.7854 (t0) cc_final: 0.7403 (t70) REVERT: B 123 ARG cc_start: 0.7825 (ttt-90) cc_final: 0.7592 (ttm-80) REVERT: C 245 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7464 (t80) REVERT: C 252 ILE cc_start: 0.7909 (mm) cc_final: 0.7608 (pt) REVERT: D 86 ASP cc_start: 0.7725 (t0) cc_final: 0.7276 (t70) REVERT: E 65 ARG cc_start: 0.7557 (mtp-110) cc_final: 0.7262 (mtm180) REVERT: E 245 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.6823 (t80) outliers start: 37 outliers final: 30 residues processed: 154 average time/residue: 0.2636 time to fit residues: 58.2108 Evaluate side-chains 157 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 125 time to evaluate : 1.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 48 optimal weight: 2.9990 chunk 130 optimal weight: 0.9980 chunk 28 optimal weight: 30.0000 chunk 85 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 120 optimal weight: 4.9990 chunk 67 optimal weight: 5.9990 chunk 12 optimal weight: 5.9990 chunk 76 optimal weight: 8.9990 chunk 139 optimal weight: 5.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 13130 Z= 0.312 Angle : 0.548 5.201 17825 Z= 0.279 Chirality : 0.049 0.213 1960 Planarity : 0.004 0.035 2250 Dihedral : 11.019 82.922 1925 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 3.35 % Allowed : 9.67 % Favored : 86.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.23), residues: 1525 helix: 1.39 (0.24), residues: 530 sheet: 0.76 (0.28), residues: 395 loop : -2.15 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 206 HIS 0.004 0.001 HIS E 177 PHE 0.013 0.002 PHE E 236 TYR 0.018 0.002 TYR B 245 ARG 0.004 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 126 time to evaluate : 1.239 Fit side-chains REVERT: A 54 LYS cc_start: 0.8744 (mttt) cc_final: 0.8460 (mtmt) REVERT: A 65 ARG cc_start: 0.7671 (mtp-110) cc_final: 0.7453 (mtp-110) REVERT: A 145 ILE cc_start: 0.9251 (OUTLIER) cc_final: 0.9030 (tt) REVERT: B 54 LYS cc_start: 0.8384 (mttt) cc_final: 0.8125 (mtmt) REVERT: B 65 ARG cc_start: 0.7783 (mtp-110) cc_final: 0.7417 (mtm180) REVERT: B 86 ASP cc_start: 0.7872 (t0) cc_final: 0.7464 (t70) REVERT: C 245 TYR cc_start: 0.7735 (OUTLIER) cc_final: 0.7445 (t80) REVERT: D 30 GLU cc_start: 0.6906 (tp30) cc_final: 0.5347 (tt0) REVERT: D 86 ASP cc_start: 0.7731 (t0) cc_final: 0.7297 (t70) REVERT: E 65 ARG cc_start: 0.7664 (mtp-110) cc_final: 0.7398 (mtm180) REVERT: E 245 TYR cc_start: 0.7800 (OUTLIER) cc_final: 0.6587 (t80) outliers start: 46 outliers final: 36 residues processed: 157 average time/residue: 0.2674 time to fit residues: 59.5531 Evaluate side-chains 162 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 123 time to evaluate : 1.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 191 ILE Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 16 optimal weight: 4.9990 chunk 82 optimal weight: 9.9990 chunk 105 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 144 optimal weight: 10.0000 chunk 90 optimal weight: 3.9990 chunk 88 optimal weight: 0.3980 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9980 chunk 57 optimal weight: 20.0000 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13130 Z= 0.200 Angle : 0.497 5.099 17825 Z= 0.252 Chirality : 0.047 0.218 1960 Planarity : 0.003 0.033 2250 Dihedral : 10.529 79.022 1925 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 3.42 % Allowed : 10.33 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.22), residues: 1525 helix: 1.44 (0.24), residues: 530 sheet: 0.78 (0.28), residues: 395 loop : -2.14 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 206 HIS 0.003 0.001 HIS E 177 PHE 0.012 0.001 PHE E 236 TYR 0.016 0.001 TYR B 245 ARG 0.002 0.000 ARG C 123 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 127 time to evaluate : 1.329 Fit side-chains REVERT: A 21 ASN cc_start: 0.7918 (t0) cc_final: 0.7708 (t0) REVERT: A 54 LYS cc_start: 0.8684 (mttt) cc_final: 0.8411 (mtmt) REVERT: A 65 ARG cc_start: 0.7619 (mtp-110) cc_final: 0.7392 (mtp-110) REVERT: A 145 ILE cc_start: 0.9204 (OUTLIER) cc_final: 0.8991 (tt) REVERT: A 263 ASP cc_start: 0.6731 (OUTLIER) cc_final: 0.6424 (m-30) REVERT: B 54 LYS cc_start: 0.8355 (mttt) cc_final: 0.8100 (mtmt) REVERT: B 65 ARG cc_start: 0.7770 (mtp-110) cc_final: 0.7415 (mtm180) REVERT: B 86 ASP cc_start: 0.7865 (t0) cc_final: 0.7452 (t70) REVERT: C 245 TYR cc_start: 0.7682 (OUTLIER) cc_final: 0.7442 (t80) REVERT: C 252 ILE cc_start: 0.8044 (mm) cc_final: 0.7693 (pt) REVERT: D 30 GLU cc_start: 0.6742 (tp30) cc_final: 0.5340 (tt0) REVERT: D 86 ASP cc_start: 0.7717 (t0) cc_final: 0.7284 (t70) REVERT: D 162 ILE cc_start: 0.8608 (mm) cc_final: 0.8291 (mm) REVERT: E 65 ARG cc_start: 0.7637 (mtp-110) cc_final: 0.7371 (mtm180) REVERT: E 145 ILE cc_start: 0.9211 (OUTLIER) cc_final: 0.8999 (tt) REVERT: E 245 TYR cc_start: 0.7670 (OUTLIER) cc_final: 0.6624 (t80) REVERT: E 263 ASP cc_start: 0.7824 (OUTLIER) cc_final: 0.7567 (m-30) REVERT: E 265 MET cc_start: 0.8045 (mtp) cc_final: 0.7716 (mtp) outliers start: 47 outliers final: 36 residues processed: 159 average time/residue: 0.2534 time to fit residues: 57.6470 Evaluate side-chains 165 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 123 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 191 ILE Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 86 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 20.0000 chunk 91 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 71 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 131 optimal weight: 2.9990 chunk 138 optimal weight: 3.9990 chunk 126 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 103 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 124 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13130 Z= 0.287 Angle : 0.543 5.337 17825 Z= 0.277 Chirality : 0.049 0.215 1960 Planarity : 0.004 0.035 2250 Dihedral : 10.620 83.400 1925 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 3.56 % Allowed : 10.18 % Favored : 86.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.23), residues: 1525 helix: 1.55 (0.24), residues: 530 sheet: 0.73 (0.28), residues: 395 loop : -2.15 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.001 TRP B 206 HIS 0.003 0.001 HIS E 177 PHE 0.016 0.001 PHE B 236 TYR 0.018 0.002 TYR B 245 ARG 0.004 0.000 ARG A 91 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 1.306 Fit side-chains REVERT: A 54 LYS cc_start: 0.8745 (mttt) cc_final: 0.8450 (mtmt) REVERT: A 65 ARG cc_start: 0.7650 (mtp-110) cc_final: 0.7425 (mtp-110) REVERT: A 145 ILE cc_start: 0.9254 (OUTLIER) cc_final: 0.9034 (tt) REVERT: A 263 ASP cc_start: 0.6957 (OUTLIER) cc_final: 0.6716 (m-30) REVERT: B 65 ARG cc_start: 0.7813 (mtp-110) cc_final: 0.7459 (mtm180) REVERT: B 86 ASP cc_start: 0.7845 (t0) cc_final: 0.7408 (t70) REVERT: C 245 TYR cc_start: 0.7702 (OUTLIER) cc_final: 0.7413 (t80) REVERT: D 30 GLU cc_start: 0.6683 (tp30) cc_final: 0.5566 (tp30) REVERT: D 86 ASP cc_start: 0.7733 (t0) cc_final: 0.7299 (t70) REVERT: D 263 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7588 (m-30) REVERT: E 65 ARG cc_start: 0.7665 (mtp-110) cc_final: 0.7411 (mtm180) REVERT: E 145 ILE cc_start: 0.9262 (OUTLIER) cc_final: 0.9057 (tt) REVERT: E 245 TYR cc_start: 0.7778 (OUTLIER) cc_final: 0.6558 (t80) REVERT: E 263 ASP cc_start: 0.7734 (OUTLIER) cc_final: 0.7497 (m-30) REVERT: E 265 MET cc_start: 0.8088 (mtp) cc_final: 0.7762 (mtp) outliers start: 49 outliers final: 36 residues processed: 152 average time/residue: 0.2629 time to fit residues: 57.0966 Evaluate side-chains 163 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 120 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 253 LEU Chi-restraints excluded: chain E residue 259 THR Chi-restraints excluded: chain E residue 263 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 134 optimal weight: 6.9990 chunk 138 optimal weight: 1.9990 chunk 81 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 chunk 41 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 142 optimal weight: 9.9990 chunk 86 optimal weight: 0.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN A 124 GLN ** A 182 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 13130 Z= 0.390 Angle : 0.600 5.916 17825 Z= 0.308 Chirality : 0.051 0.213 1960 Planarity : 0.004 0.037 2250 Dihedral : 10.959 92.213 1925 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.56 % Allowed : 10.47 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.23), residues: 1525 helix: 1.56 (0.24), residues: 530 sheet: 0.94 (0.30), residues: 345 loop : -2.20 (0.23), residues: 650 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 206 HIS 0.004 0.001 HIS E 177 PHE 0.016 0.002 PHE E 236 TYR 0.021 0.002 TYR B 245 ARG 0.005 0.001 ARG E 91 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 120 time to evaluate : 1.405 Fit side-chains REVERT: A 54 LYS cc_start: 0.8762 (mttt) cc_final: 0.8434 (mtmt) REVERT: A 65 ARG cc_start: 0.7645 (mtp-110) cc_final: 0.7420 (mtp-110) REVERT: B 65 ARG cc_start: 0.7805 (mtp-110) cc_final: 0.7498 (mtm180) REVERT: B 86 ASP cc_start: 0.7856 (t0) cc_final: 0.7442 (t70) REVERT: C 245 TYR cc_start: 0.7745 (OUTLIER) cc_final: 0.7406 (t80) REVERT: D 86 ASP cc_start: 0.7738 (t0) cc_final: 0.7314 (t70) REVERT: D 263 ASP cc_start: 0.7780 (OUTLIER) cc_final: 0.7478 (m-30) REVERT: E 65 ARG cc_start: 0.7696 (mtp-110) cc_final: 0.7425 (mtm180) REVERT: E 145 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.9083 (tt) REVERT: E 245 TYR cc_start: 0.7910 (OUTLIER) cc_final: 0.6534 (t80) outliers start: 49 outliers final: 38 residues processed: 154 average time/residue: 0.2682 time to fit residues: 58.8524 Evaluate side-chains 158 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 116 time to evaluate : 1.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 84 SER Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 238 LEU Chi-restraints excluded: chain A residue 245 TYR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 278 LEU Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 84 SER Chi-restraints excluded: chain B residue 134 SER Chi-restraints excluded: chain B residue 238 LEU Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 30 GLU Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 107 LEU Chi-restraints excluded: chain C residue 134 SER Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 245 TYR Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 60 ASN Chi-restraints excluded: chain D residue 84 SER Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 145 ILE Chi-restraints excluded: chain D residue 180 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 67 optimal weight: 0.0870 chunk 99 optimal weight: 2.9990 chunk 149 optimal weight: 4.9990 chunk 137 optimal weight: 3.9990 chunk 118 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 91 optimal weight: 0.0570 chunk 72 optimal weight: 0.7980 chunk 94 optimal weight: 0.7980 chunk 126 optimal weight: 0.8980 chunk 36 optimal weight: 0.9980 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 13130 Z= 0.130 Angle : 0.477 5.378 17825 Z= 0.242 Chirality : 0.047 0.221 1960 Planarity : 0.003 0.032 2250 Dihedral : 9.974 75.652 1925 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 2.84 % Allowed : 11.20 % Favored : 85.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.23), residues: 1525 helix: 1.72 (0.24), residues: 525 sheet: 0.82 (0.28), residues: 395 loop : -2.24 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP B 206 HIS 0.002 0.001 HIS C 177 PHE 0.013 0.001 PHE B 236 TYR 0.014 0.001 TYR B 245 ARG 0.003 0.000 ARG C 123 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3050 Ramachandran restraints generated. 1525 Oldfield, 0 Emsley, 1525 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 131 time to evaluate : 1.202 Fit side-chains REVERT: A 54 LYS cc_start: 0.8678 (mttt) cc_final: 0.8385 (mtmt) REVERT: A 65 ARG cc_start: 0.7560 (mtp-110) cc_final: 0.7332 (mtp-110) REVERT: A 145 ILE cc_start: 0.9153 (OUTLIER) cc_final: 0.8932 (tt) REVERT: A 187 GLU cc_start: 0.7269 (tt0) cc_final: 0.7046 (tt0) REVERT: B 65 ARG cc_start: 0.7749 (mtp-110) cc_final: 0.7430 (mtm180) REVERT: B 86 ASP cc_start: 0.7843 (t0) cc_final: 0.7406 (t70) REVERT: D 30 GLU cc_start: 0.7054 (mp0) cc_final: 0.5707 (tp30) REVERT: D 86 ASP cc_start: 0.7722 (t0) cc_final: 0.7276 (t70) REVERT: D 162 ILE cc_start: 0.8581 (mm) cc_final: 0.8329 (mm) REVERT: D 263 ASP cc_start: 0.7395 (OUTLIER) cc_final: 0.7054 (m-30) REVERT: E 65 ARG cc_start: 0.7603 (mtp-110) cc_final: 0.7364 (mtm180) REVERT: E 145 ILE cc_start: 0.9157 (OUTLIER) cc_final: 0.8941 (tt) REVERT: E 245 TYR cc_start: 0.7567 (OUTLIER) cc_final: 0.6783 (t80) outliers start: 39 outliers final: 24 residues processed: 156 average time/residue: 0.2940 time to fit residues: 66.1772 Evaluate side-chains 155 residues out of total 1375 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 127 time to evaluate : 1.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 THR Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain B residue 60 ASN Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain B residue 245 TYR Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 263 ASP Chi-restraints excluded: chain B residue 278 LEU Chi-restraints excluded: chain C residue 145 ILE Chi-restraints excluded: chain C residue 180 SER Chi-restraints excluded: chain C residue 191 ILE Chi-restraints excluded: chain C residue 259 THR Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain D residue 107 LEU Chi-restraints excluded: chain D residue 134 SER Chi-restraints excluded: chain D residue 263 ASP Chi-restraints excluded: chain D residue 278 LEU Chi-restraints excluded: chain E residue 29 LEU Chi-restraints excluded: chain E residue 60 ASN Chi-restraints excluded: chain E residue 93 MET Chi-restraints excluded: chain E residue 134 SER Chi-restraints excluded: chain E residue 145 ILE Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 245 TYR Chi-restraints excluded: chain E residue 259 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 150 random chunks: chunk 109 optimal weight: 5.9990 chunk 17 optimal weight: 0.2980 chunk 33 optimal weight: 0.7980 chunk 119 optimal weight: 9.9990 chunk 49 optimal weight: 4.9990 chunk 122 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 21 optimal weight: 0.8980 chunk 104 optimal weight: 9.9990 chunk 6 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- 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 = 0.3642 r_free = 0.3642 target = 0.154597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3141 r_free = 0.3141 target = 0.111251 restraints weight = 13077.528| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 1.59 r_work: 0.3103 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8242 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 13130 Z= 0.252 Angle : 0.525 5.305 17825 Z= 0.267 Chirality : 0.049 0.217 1960 Planarity : 0.003 0.035 2250 Dihedral : 10.082 78.786 1925 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.33 % Allowed : 11.64 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.23), residues: 1525 helix: 1.78 (0.24), residues: 525 sheet: 0.78 (0.28), residues: 395 loop : -2.25 (0.24), residues: 605 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP B 206 HIS 0.003 0.001 HIS A 177 PHE 0.013 0.001 PHE E 236 TYR 0.018 0.001 TYR B 245 ARG 0.003 0.000 ARG A 91 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2343.62 seconds wall clock time: 43 minutes 8.19 seconds (2588.19 seconds total)