Starting phenix.real_space_refine on Mon Jun 9 17:38:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbg_37424/06_2025/8wbg_37424_neut.cif" } resolution = 3.2 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= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6811 2.51 5 N 1947 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2759 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 1 Chain: "a" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 7.48, per 1000 atoms: 0.69 Number of scatterers: 10854 At special positions: 0 Unit cell: (109.65, 121.55, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2016 8.00 N 1947 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 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: 3.00 Conformation dependent library (CDL) restraints added in 1.7 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 19.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.08 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.086A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.923A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.681A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.544A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.615A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.066A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.828A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 77 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU a 80 " --> pdb=" O ASN a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.597A pdb=" N TRP b 28 " --> pdb=" O VAL b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 removed outlier: 4.368A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN b 76 " --> pdb=" O GLU b 72 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA b 77 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.611A pdb=" N LEU b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.659A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.501A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.531A pdb=" N ASP A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU A 12 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.672A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.118A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.509A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.616A pdb=" N GLU A 274 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 203 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 193 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE a 323 " --> pdb=" O TRP a 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 removed outlier: 3.659A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU b 12 " --> pdb=" O ASP b 7 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.658A pdb=" N HIS B 35 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.748A pdb=" N GLU B 274 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 204 " --> pdb=" O ALA b 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.109A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'a' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AB6, first strand: chain 'b' and resid 87 through 89 Processing sheet with id=AB7, first strand: chain 'b' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'b' and resid 284 through 287 removed outlier: 3.787A pdb=" N TRP b 311 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS b 313 " --> pdb=" O HIS b 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 298 through 299 removed outlier: 3.634A pdb=" N LEU b 298 " --> pdb=" O TYR b 331 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 726 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: 3.52 Time building geometry restraints manager: 3.60 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: 3609 1.35 - 1.47: 2674 1.47 - 1.59: 4750 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 11145 Sorted by residual: bond pdb=" N VAL b 162 " pdb=" CA VAL b 162 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N PHE b 160 " pdb=" CA PHE b 160 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.30e-02 5.92e+03 5.59e+00 bond pdb=" N ASP A 24 " pdb=" CA ASP A 24 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.42e-02 4.96e+03 5.42e+00 bond pdb=" N ASN a 207 " pdb=" CA ASN a 207 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.42e+00 ... (remaining 11140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 14516 1.32 - 2.65: 479 2.65 - 3.97: 95 3.97 - 5.29: 14 5.29 - 6.62: 2 Bond angle restraints: 15106 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 112.72 107.72 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA TRP A 28 " pdb=" C TRP A 28 " pdb=" N ARG A 29 " ideal model delta sigma weight residual 118.13 123.11 -4.98 1.28e+00 6.10e-01 1.51e+01 angle pdb=" N ILE b 242 " pdb=" CA ILE b 242 " pdb=" C ILE b 242 " ideal model delta sigma weight residual 111.48 107.94 3.54 9.40e-01 1.13e+00 1.42e+01 angle pdb=" CA ASP A 24 " pdb=" C ASP A 24 " pdb=" O ASP A 24 " ideal model delta sigma weight residual 122.27 117.95 4.32 1.16e+00 7.43e-01 1.39e+01 angle pdb=" C ASN a 207 " pdb=" CA ASN a 207 " pdb=" CB ASN a 207 " ideal model delta sigma weight residual 110.42 117.04 -6.62 1.99e+00 2.53e-01 1.11e+01 ... (remaining 15101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6135 17.60 - 35.19: 444 35.19 - 52.79: 91 52.79 - 70.39: 24 70.39 - 87.98: 7 Dihedral angle restraints: 6701 sinusoidal: 2816 harmonic: 3885 Sorted by residual: dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS b 313 " pdb=" SG CYS b 313 " pdb=" SG CYS b 316 " pdb=" CB CYS b 316 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1235 0.043 - 0.085: 214 0.085 - 0.128: 126 0.128 - 0.170: 7 0.170 - 0.213: 2 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL b 162 " pdb=" N VAL b 162 " pdb=" C VAL b 162 " pdb=" CB VAL b 162 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1581 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 101 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ASP a 208 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.011 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN b 95 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO b 96 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO b 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 96 " 0.019 5.00e-02 4.00e+02 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 837 2.74 - 3.28: 10584 3.28 - 3.82: 16278 3.82 - 4.36: 20013 4.36 - 4.90: 36068 Nonbonded interactions: 83780 Sorted by model distance: nonbonded pdb=" OG SER B 322 " pdb=" NH1 ARG B 324 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG b 299 " pdb=" O THR b 301 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 61 " pdb=" OE1 GLU B 219 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU a 72 " pdb=" ND2 ASN a 76 " model vdw 2.236 3.120 nonbonded pdb=" OG SER b 322 " pdb=" NH1 ARG b 324 " model vdw 2.243 3.120 ... (remaining 83775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352)) selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.480 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 29.900 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.040 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: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 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 0.038 11169 Z= 0.154 Angle : 0.585 6.617 15154 Z= 0.344 Chirality : 0.042 0.213 1584 Planarity : 0.004 0.047 1945 Dihedral : 13.023 87.838 4123 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.10 (0.24), residues: 1343 helix: 1.10 (0.44), residues: 148 sheet: -1.73 (0.36), residues: 225 loop : -0.78 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 232 HIS 0.004 0.001 HIS b 254 PHE 0.011 0.001 PHE A 123 TYR 0.010 0.001 TYR B 32 ARG 0.002 0.000 ARG a 338 Details of bonding type rmsd hydrogen bonds : bond 0.22758 ( 295) hydrogen bonds : angle 8.92144 ( 726) SS BOND : bond 0.00253 ( 24) SS BOND : angle 1.22673 ( 48) covalent geometry : bond 0.00280 (11145) covalent geometry : angle 0.58232 (15106) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 204 time to evaluate : 1.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7669 (tpp80) REVERT: A 156 GLU cc_start: 0.7451 (pt0) cc_final: 0.7196 (pt0) REVERT: A 274 GLU cc_start: 0.8077 (tt0) cc_final: 0.7687 (mt-10) REVERT: a 207 ASN cc_start: 0.7381 (t0) cc_final: 0.6814 (t0) REVERT: a 208 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6865 (t0) REVERT: a 251 LEU cc_start: 0.8657 (mp) cc_final: 0.8389 (mp) REVERT: a 315 GLU cc_start: 0.8065 (tt0) cc_final: 0.7557 (tp30) REVERT: b 67 MET cc_start: 0.6248 (tmm) cc_final: 0.6040 (tmm) REVERT: b 330 TRP cc_start: 0.6650 (m100) cc_final: 0.6196 (m-10) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2967 time to fit residues: 81.3390 Evaluate side-chains 121 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 120 time to evaluate : 1.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 147 HIS A 207 ASN B 35 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN a 76 ASN a 207 ASN b 35 HIS b 269 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4363 r_free = 0.4363 target = 0.208210 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.165632 restraints weight = 12265.608| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 3.34 r_work: 0.3675 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 11169 Z= 0.204 Angle : 0.656 7.239 15154 Z= 0.347 Chirality : 0.046 0.178 1584 Planarity : 0.005 0.048 1945 Dihedral : 5.322 51.266 1478 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.96 % Favored : 93.89 % Rotamer: Outliers : 1.60 % Allowed : 7.49 % Favored : 90.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.24), residues: 1343 helix: 0.97 (0.41), residues: 159 sheet: -1.76 (0.32), residues: 279 loop : -0.82 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP a 232 HIS 0.007 0.001 HIS b 254 PHE 0.026 0.002 PHE B 277 TYR 0.018 0.002 TYR a 331 ARG 0.005 0.001 ARG A 261 Details of bonding type rmsd hydrogen bonds : bond 0.04497 ( 295) hydrogen bonds : angle 6.47318 ( 726) SS BOND : bond 0.00396 ( 24) SS BOND : angle 1.68573 ( 48) covalent geometry : bond 0.00494 (11145) covalent geometry : angle 0.65048 (15106) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 139 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6539 (t0) cc_final: 0.6322 (t0) REVERT: A 97 MET cc_start: 0.8512 (mtm) cc_final: 0.8218 (mtt) REVERT: A 333 MET cc_start: 0.6271 (OUTLIER) cc_final: 0.5727 (mtp) REVERT: B 339 LYS cc_start: 0.7343 (pttm) cc_final: 0.6810 (ptmm) REVERT: a 69 ARG cc_start: 0.7139 (ptp-170) cc_final: 0.6736 (tpp80) REVERT: a 146 LYS cc_start: 0.8061 (mtpt) cc_final: 0.7803 (mmtt) REVERT: b 67 MET cc_start: 0.5881 (tmm) cc_final: 0.5590 (tmm) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.3204 time to fit residues: 67.4566 Evaluate side-chains 130 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 115 time to evaluate : 1.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 77 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 92 optimal weight: 6.9990 chunk 118 optimal weight: 1.9990 chunk 93 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 129 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 5.9990 chunk 97 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 254 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.205681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.164766 restraints weight = 12365.430| |-----------------------------------------------------------------------------| r_work (start): 0.3940 rms_B_bonded: 3.35 r_work: 0.3664 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 11169 Z= 0.192 Angle : 0.644 11.033 15154 Z= 0.337 Chirality : 0.045 0.274 1584 Planarity : 0.004 0.044 1945 Dihedral : 4.981 21.698 1476 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 4.55 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.44 % Favored : 94.49 % Rotamer: Outliers : 2.61 % Allowed : 10.18 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.30 (0.23), residues: 1343 helix: 1.01 (0.42), residues: 159 sheet: -1.74 (0.31), residues: 295 loop : -0.89 (0.21), residues: 889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 311 HIS 0.007 0.001 HIS b 254 PHE 0.022 0.002 PHE B 277 TYR 0.016 0.002 TYR A 331 ARG 0.004 0.000 ARG a 324 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 295) hydrogen bonds : angle 6.22050 ( 726) SS BOND : bond 0.00386 ( 24) SS BOND : angle 2.12505 ( 48) covalent geometry : bond 0.00464 (11145) covalent geometry : angle 0.63381 (15106) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 125 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6705 (t0) cc_final: 0.6494 (t0) REVERT: A 97 MET cc_start: 0.8466 (mtm) cc_final: 0.8143 (mtt) REVERT: A 156 GLU cc_start: 0.7469 (pt0) cc_final: 0.7168 (pt0) REVERT: A 274 GLU cc_start: 0.8280 (tt0) cc_final: 0.8066 (tt0) REVERT: A 324 ARG cc_start: 0.8380 (mpt180) cc_final: 0.8094 (mmt90) REVERT: B 333 MET cc_start: 0.6930 (mtt) cc_final: 0.6449 (mtm) REVERT: B 339 LYS cc_start: 0.7335 (pttm) cc_final: 0.6953 (ptmm) REVERT: a 34 TYR cc_start: 0.7498 (m-80) cc_final: 0.7268 (m-80) REVERT: a 146 LYS cc_start: 0.8124 (mtpt) cc_final: 0.7836 (mmtm) REVERT: a 324 ARG cc_start: 0.8497 (mmt-90) cc_final: 0.8204 (mmt-90) REVERT: a 333 MET cc_start: 0.8187 (mmp) cc_final: 0.7984 (mmp) REVERT: b 67 MET cc_start: 0.5974 (tmm) cc_final: 0.5646 (tmm) outliers start: 31 outliers final: 20 residues processed: 145 average time/residue: 0.2576 time to fit residues: 52.9403 Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 1.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 56 optimal weight: 2.9990 chunk 85 optimal weight: 0.1980 chunk 11 optimal weight: 5.9990 chunk 111 optimal weight: 3.9990 chunk 106 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.205482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.164836 restraints weight = 12285.587| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 3.39 r_work: 0.3637 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11169 Z= 0.171 Angle : 0.612 14.190 15154 Z= 0.318 Chirality : 0.044 0.231 1584 Planarity : 0.004 0.043 1945 Dihedral : 4.826 19.404 1476 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.88 % Favored : 93.97 % Rotamer: Outliers : 3.11 % Allowed : 11.02 % Favored : 85.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.36 (0.23), residues: 1343 helix: 1.01 (0.42), residues: 159 sheet: -1.59 (0.31), residues: 313 loop : -1.00 (0.21), residues: 871 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP a 330 HIS 0.006 0.001 HIS B 254 PHE 0.019 0.002 PHE B 277 TYR 0.015 0.001 TYR A 331 ARG 0.005 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03818 ( 295) hydrogen bonds : angle 6.01591 ( 726) SS BOND : bond 0.00430 ( 24) SS BOND : angle 1.84215 ( 48) covalent geometry : bond 0.00413 (11145) covalent geometry : angle 0.60384 (15106) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 134 time to evaluate : 1.562 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8401 (tpp80) cc_final: 0.8013 (tpp80) REVERT: A 52 ASP cc_start: 0.6748 (t0) cc_final: 0.6499 (t0) REVERT: A 97 MET cc_start: 0.8464 (mtm) cc_final: 0.8129 (mtt) REVERT: A 156 GLU cc_start: 0.7500 (pt0) cc_final: 0.7202 (pt0) REVERT: A 324 ARG cc_start: 0.8408 (mpt180) cc_final: 0.8128 (mmt90) REVERT: B 263 GLN cc_start: 0.7145 (mp10) cc_final: 0.6882 (mt0) REVERT: B 333 MET cc_start: 0.6863 (mtt) cc_final: 0.6555 (mtm) REVERT: B 339 LYS cc_start: 0.7422 (pttm) cc_final: 0.7106 (ptmm) REVERT: a 34 TYR cc_start: 0.7553 (m-80) cc_final: 0.7306 (m-80) REVERT: a 146 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7931 (mmtm) REVERT: a 324 ARG cc_start: 0.8431 (mmt-90) cc_final: 0.8224 (mmt-90) REVERT: b 67 MET cc_start: 0.5924 (tmm) cc_final: 0.5606 (tmm) REVERT: b 265 LYS cc_start: 0.7018 (mtpt) cc_final: 0.6512 (mtpt) outliers start: 37 outliers final: 28 residues processed: 161 average time/residue: 0.3743 time to fit residues: 88.3051 Evaluate side-chains 149 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 121 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 19 optimal weight: 4.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 2.9990 chunk 84 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 81 optimal weight: 0.0470 chunk 31 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 overall best weight: 1.9282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4336 r_free = 0.4336 target = 0.205267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3960 r_free = 0.3960 target = 0.164342 restraints weight = 12188.610| |-----------------------------------------------------------------------------| r_work (start): 0.3933 rms_B_bonded: 3.26 r_work: 0.3667 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 11169 Z= 0.175 Angle : 0.612 13.352 15154 Z= 0.318 Chirality : 0.044 0.228 1584 Planarity : 0.004 0.041 1945 Dihedral : 4.800 21.794 1476 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 3.70 % Allowed : 12.20 % Favored : 84.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.44 (0.23), residues: 1343 helix: 0.95 (0.41), residues: 159 sheet: -1.52 (0.33), residues: 285 loop : -1.15 (0.21), residues: 899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP b 68 HIS 0.006 0.001 HIS B 254 PHE 0.018 0.002 PHE B 277 TYR 0.014 0.001 TYR A 331 ARG 0.008 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03749 ( 295) hydrogen bonds : angle 5.94430 ( 726) SS BOND : bond 0.00426 ( 24) SS BOND : angle 1.76214 ( 48) covalent geometry : bond 0.00424 (11145) covalent geometry : angle 0.60493 (15106) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 122 time to evaluate : 1.625 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8563 (t0) cc_final: 0.8323 (t0) REVERT: A 28 TRP cc_start: 0.7203 (m-10) cc_final: 0.6571 (m-10) REVERT: A 97 MET cc_start: 0.8488 (mtm) cc_final: 0.8157 (mtt) REVERT: A 156 GLU cc_start: 0.7481 (pt0) cc_final: 0.7191 (pt0) REVERT: A 324 ARG cc_start: 0.8399 (mpt180) cc_final: 0.8081 (mmt90) REVERT: B 333 MET cc_start: 0.6931 (mtt) cc_final: 0.6657 (mtm) REVERT: B 339 LYS cc_start: 0.7647 (pttm) cc_final: 0.7368 (ptmm) REVERT: a 34 TYR cc_start: 0.7546 (m-80) cc_final: 0.7295 (m-80) REVERT: a 69 ARG cc_start: 0.7179 (ptp-170) cc_final: 0.6677 (tpp80) REVERT: a 146 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7945 (mmtm) REVERT: a 311 TRP cc_start: 0.6638 (m100) cc_final: 0.6221 (m100) REVERT: a 324 ARG cc_start: 0.8422 (mmt-90) cc_final: 0.8190 (mmt-90) REVERT: a 333 MET cc_start: 0.7949 (mmp) cc_final: 0.7398 (mmp) REVERT: b 67 MET cc_start: 0.6046 (tmm) cc_final: 0.5708 (tmm) REVERT: b 265 LYS cc_start: 0.7037 (mtpt) cc_final: 0.6548 (mtpt) outliers start: 44 outliers final: 33 residues processed: 155 average time/residue: 0.2668 time to fit residues: 58.9623 Evaluate side-chains 151 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 118 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 8.9990 chunk 87 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 chunk 89 optimal weight: 0.5980 chunk 49 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 131 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 100 optimal weight: 1.9990 chunk 129 optimal weight: 6.9990 overall best weight: 4.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 85 GLN B 95 ASN ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.199505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.159048 restraints weight = 12448.943| |-----------------------------------------------------------------------------| r_work (start): 0.3879 rms_B_bonded: 3.32 r_work: 0.3596 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 moved from start: 0.2861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.077 11169 Z= 0.332 Angle : 0.782 14.844 15154 Z= 0.408 Chirality : 0.051 0.247 1584 Planarity : 0.005 0.051 1945 Dihedral : 5.536 28.031 1476 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.15 % Allowed : 9.01 % Favored : 90.84 % Rotamer: Outliers : 3.95 % Allowed : 13.88 % Favored : 82.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.99 (0.23), residues: 1343 helix: 0.49 (0.40), residues: 159 sheet: -1.91 (0.31), residues: 297 loop : -1.50 (0.20), residues: 887 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 311 HIS 0.011 0.002 HIS B 254 PHE 0.019 0.003 PHE A 133 TYR 0.017 0.002 TYR B 34 ARG 0.009 0.001 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.04851 ( 295) hydrogen bonds : angle 6.54586 ( 726) SS BOND : bond 0.00612 ( 24) SS BOND : angle 2.49661 ( 48) covalent geometry : bond 0.00797 (11145) covalent geometry : angle 0.77044 (15106) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 122 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8540 (mtm) cc_final: 0.8218 (mtt) REVERT: A 156 GLU cc_start: 0.7563 (pt0) cc_final: 0.7274 (pt0) REVERT: B 339 LYS cc_start: 0.7606 (pttm) cc_final: 0.7308 (ptmm) REVERT: a 34 TYR cc_start: 0.7649 (m-80) cc_final: 0.7369 (m-80) REVERT: a 69 ARG cc_start: 0.7227 (ptp-170) cc_final: 0.6790 (tpp80) REVERT: a 146 LYS cc_start: 0.8208 (mtpt) cc_final: 0.7964 (mmtm) REVERT: a 217 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.7727 (mt) REVERT: a 333 MET cc_start: 0.8145 (mmp) cc_final: 0.7702 (mmp) REVERT: b 265 LYS cc_start: 0.7161 (mtpt) cc_final: 0.6708 (mtpt) outliers start: 47 outliers final: 38 residues processed: 158 average time/residue: 0.2403 time to fit residues: 54.4911 Evaluate side-chains 150 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 111 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 115 TRP Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 17 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 174 ASP Chi-restraints excluded: chain a residue 217 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.7980 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 0.0170 chunk 118 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 95 ASN a 344 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.208284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167562 restraints weight = 12450.183| |-----------------------------------------------------------------------------| r_work (start): 0.3957 rms_B_bonded: 3.39 r_work: 0.3681 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.2996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 11169 Z= 0.115 Angle : 0.598 11.877 15154 Z= 0.307 Chirality : 0.042 0.202 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.565 18.456 1476 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.24 % Favored : 95.61 % Rotamer: Outliers : 2.27 % Allowed : 15.98 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.55 (0.23), residues: 1343 helix: 0.78 (0.40), residues: 160 sheet: -1.74 (0.32), residues: 281 loop : -1.14 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 311 HIS 0.004 0.001 HIS b 147 PHE 0.016 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.008 0.000 ARG b 14 Details of bonding type rmsd hydrogen bonds : bond 0.03186 ( 295) hydrogen bonds : angle 5.76563 ( 726) SS BOND : bond 0.00437 ( 24) SS BOND : angle 1.92591 ( 48) covalent geometry : bond 0.00275 (11145) covalent geometry : angle 0.58926 (15106) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 128 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8336 (tpp80) cc_final: 0.8123 (tpp80) REVERT: A 97 MET cc_start: 0.8441 (mtm) cc_final: 0.8211 (mtm) REVERT: A 99 ARG cc_start: 0.7999 (ttm170) cc_final: 0.7586 (ttm170) REVERT: A 156 GLU cc_start: 0.7508 (pt0) cc_final: 0.7190 (pt0) REVERT: A 205 GLU cc_start: 0.7746 (tp30) cc_final: 0.7537 (tp30) REVERT: A 324 ARG cc_start: 0.8329 (mpt180) cc_final: 0.8115 (mmt90) REVERT: B 339 LYS cc_start: 0.7705 (pttm) cc_final: 0.7427 (ptmm) REVERT: a 69 ARG cc_start: 0.7138 (ptp-170) cc_final: 0.6603 (tpp80) REVERT: a 95 ASN cc_start: 0.8212 (m110) cc_final: 0.7939 (m110) REVERT: a 146 LYS cc_start: 0.8222 (mtpt) cc_final: 0.7943 (mmtm) REVERT: a 333 MET cc_start: 0.8091 (mmp) cc_final: 0.7762 (mmp) REVERT: b 67 MET cc_start: 0.6021 (tmm) cc_final: 0.5729 (tmm) REVERT: b 265 LYS cc_start: 0.6916 (mtpt) cc_final: 0.6477 (mtpt) REVERT: b 349 MET cc_start: 0.3280 (ptp) cc_final: 0.3005 (ptp) outliers start: 27 outliers final: 19 residues processed: 148 average time/residue: 0.2393 time to fit residues: 49.9379 Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 120 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 0.9990 chunk 49 optimal weight: 0.0270 chunk 124 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 105 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 102 optimal weight: 0.9980 chunk 2 optimal weight: 0.3980 chunk 54 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 overall best weight: 0.5040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN b 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.210039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.169344 restraints weight = 12161.934| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 3.24 r_work: 0.3722 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7504 moved from start: 0.3135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11169 Z= 0.105 Angle : 0.584 13.055 15154 Z= 0.296 Chirality : 0.042 0.174 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.314 16.323 1476 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.77 % Favored : 95.09 % Rotamer: Outliers : 1.93 % Allowed : 16.23 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.38 (0.23), residues: 1343 helix: 0.89 (0.41), residues: 160 sheet: -1.68 (0.32), residues: 281 loop : -1.00 (0.21), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 68 HIS 0.004 0.001 HIS B 269 PHE 0.016 0.001 PHE B 277 TYR 0.010 0.001 TYR b 200 ARG 0.007 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03011 ( 295) hydrogen bonds : angle 5.63194 ( 726) SS BOND : bond 0.00390 ( 24) SS BOND : angle 1.70439 ( 48) covalent geometry : bond 0.00250 (11145) covalent geometry : angle 0.57742 (15106) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 29 ARG cc_start: 0.7788 (mpt90) cc_final: 0.7553 (mmt-90) REVERT: A 99 ARG cc_start: 0.7976 (ttm170) cc_final: 0.7596 (ttm170) REVERT: A 156 GLU cc_start: 0.7483 (pt0) cc_final: 0.7158 (pt0) REVERT: A 205 GLU cc_start: 0.7672 (tp30) cc_final: 0.7424 (tp30) REVERT: B 141 LYS cc_start: 0.7585 (pptt) cc_final: 0.6896 (ttpp) REVERT: B 339 LYS cc_start: 0.7722 (pttm) cc_final: 0.7414 (ptmm) REVERT: a 33 LYS cc_start: 0.6973 (tppt) cc_final: 0.6068 (tmtt) REVERT: a 69 ARG cc_start: 0.7151 (ptp-170) cc_final: 0.6602 (tpp80) REVERT: a 146 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7920 (mmtm) REVERT: a 333 MET cc_start: 0.8036 (mmp) cc_final: 0.7755 (mmp) REVERT: b 67 MET cc_start: 0.5986 (tmm) cc_final: 0.5641 (tmm) REVERT: b 349 MET cc_start: 0.3198 (ptp) cc_final: 0.2907 (ptp) outliers start: 23 outliers final: 20 residues processed: 148 average time/residue: 0.2619 time to fit residues: 54.8126 Evaluate side-chains 137 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 117 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 9.9990 chunk 19 optimal weight: 6.9990 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 114 optimal weight: 30.0000 chunk 61 optimal weight: 1.9990 chunk 22 optimal weight: 0.0670 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 5.9990 chunk 100 optimal weight: 0.2980 chunk 78 optimal weight: 0.0970 overall best weight: 0.6718 ------------------------------------------------------------------------------- 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 = 0.4372 r_free = 0.4372 target = 0.210419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.169205 restraints weight = 12294.176| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 3.58 r_work: 0.3705 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11169 Z= 0.109 Angle : 0.582 12.848 15154 Z= 0.296 Chirality : 0.042 0.173 1584 Planarity : 0.004 0.037 1945 Dihedral : 4.194 16.004 1476 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.21 % Favored : 94.64 % Rotamer: Outliers : 1.85 % Allowed : 16.65 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.29 (0.24), residues: 1343 helix: 0.93 (0.41), residues: 160 sheet: -1.60 (0.32), residues: 289 loop : -0.93 (0.22), residues: 894 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 311 HIS 0.003 0.001 HIS b 195 PHE 0.015 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.006 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03022 ( 295) hydrogen bonds : angle 5.53331 ( 726) SS BOND : bond 0.00473 ( 24) SS BOND : angle 1.72653 ( 48) covalent geometry : bond 0.00261 (11145) covalent geometry : angle 0.57525 (15106) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 124 time to evaluate : 2.327 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 99 ARG cc_start: 0.7961 (ttm170) cc_final: 0.7566 (ttm170) REVERT: A 125 ARG cc_start: 0.8321 (mtp85) cc_final: 0.7904 (mmm-85) REVERT: A 156 GLU cc_start: 0.7457 (pt0) cc_final: 0.7113 (pt0) REVERT: A 205 GLU cc_start: 0.7709 (tp30) cc_final: 0.7400 (tp30) REVERT: B 141 LYS cc_start: 0.7575 (pptt) cc_final: 0.6938 (ttpp) REVERT: B 339 LYS cc_start: 0.7735 (pttm) cc_final: 0.7377 (ptmm) REVERT: a 33 LYS cc_start: 0.6905 (tppt) cc_final: 0.5978 (tmtt) REVERT: a 69 ARG cc_start: 0.7137 (ptp-170) cc_final: 0.6485 (tpp80) REVERT: a 146 LYS cc_start: 0.8280 (mtpt) cc_final: 0.7924 (mmtm) REVERT: a 333 MET cc_start: 0.8034 (mmp) cc_final: 0.7732 (mmp) REVERT: b 264 MET cc_start: 0.6325 (tpp) cc_final: 0.6057 (tpp) outliers start: 22 outliers final: 20 residues processed: 141 average time/residue: 0.3296 time to fit residues: 65.5546 Evaluate side-chains 139 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 119 time to evaluate : 3.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 209 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 5.9990 chunk 102 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 9.9990 chunk 76 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 52 optimal weight: 0.1980 chunk 83 optimal weight: 4.9990 chunk 92 optimal weight: 0.9980 chunk 134 optimal weight: 10.0000 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.4371 r_free = 0.4371 target = 0.210163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.168885 restraints weight = 12192.706| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 3.60 r_work: 0.3698 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 11169 Z= 0.115 Angle : 0.588 12.948 15154 Z= 0.299 Chirality : 0.042 0.173 1584 Planarity : 0.004 0.037 1945 Dihedral : 4.172 16.033 1476 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.51 % Favored : 94.34 % Rotamer: Outliers : 1.77 % Allowed : 16.57 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.29 (0.24), residues: 1343 helix: 0.92 (0.41), residues: 160 sheet: -1.67 (0.32), residues: 279 loop : -0.92 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 28 HIS 0.003 0.001 HIS b 254 PHE 0.014 0.001 PHE B 277 TYR 0.011 0.001 TYR b 200 ARG 0.007 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03041 ( 295) hydrogen bonds : angle 5.51747 ( 726) SS BOND : bond 0.00445 ( 24) SS BOND : angle 1.73413 ( 48) covalent geometry : bond 0.00276 (11145) covalent geometry : angle 0.58085 (15106) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 124 time to evaluate : 2.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8530 (t0) cc_final: 0.8188 (t0) REVERT: A 99 ARG cc_start: 0.7970 (ttm170) cc_final: 0.7528 (ttm170) REVERT: A 125 ARG cc_start: 0.8308 (mtp85) cc_final: 0.7890 (mmm-85) REVERT: A 156 GLU cc_start: 0.7460 (pt0) cc_final: 0.7141 (pt0) REVERT: A 205 GLU cc_start: 0.7720 (tp30) cc_final: 0.7408 (tp30) REVERT: B 141 LYS cc_start: 0.7544 (pptt) cc_final: 0.6901 (ttpp) REVERT: B 339 LYS cc_start: 0.7734 (pttm) cc_final: 0.7377 (ptmm) REVERT: a 33 LYS cc_start: 0.6903 (tppt) cc_final: 0.5968 (tmtt) REVERT: a 69 ARG cc_start: 0.7138 (ptp-170) cc_final: 0.6431 (tpp80) REVERT: a 146 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7916 (mmtm) REVERT: a 333 MET cc_start: 0.8047 (mmp) cc_final: 0.7802 (mmp) REVERT: b 264 MET cc_start: 0.6341 (tpp) cc_final: 0.6076 (tpp) outliers start: 21 outliers final: 20 residues processed: 141 average time/residue: 0.4297 time to fit residues: 89.6533 Evaluate side-chains 140 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 1.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 209 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 3.9990 chunk 122 optimal weight: 0.8980 chunk 96 optimal weight: 3.9990 chunk 127 optimal weight: 0.0870 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 0.0040 chunk 38 optimal weight: 0.9990 chunk 22 optimal weight: 0.6980 chunk 125 optimal weight: 10.0000 chunk 74 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 overall best weight: 0.5372 ------------------------------------------------------------------------------- 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 = 0.4401 r_free = 0.4401 target = 0.213445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.171571 restraints weight = 12245.596| |-----------------------------------------------------------------------------| r_work (start): 0.4000 rms_B_bonded: 3.49 r_work: 0.3732 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 11169 Z= 0.104 Angle : 0.578 12.650 15154 Z= 0.292 Chirality : 0.042 0.172 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.031 16.936 1476 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.62 % Favored : 95.23 % Rotamer: Outliers : 1.51 % Allowed : 17.33 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % 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: -1.20 (0.24), residues: 1343 helix: 0.88 (0.41), residues: 160 sheet: -1.63 (0.33), residues: 279 loop : -0.82 (0.22), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 28 HIS 0.004 0.001 HIS b 195 PHE 0.014 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.007 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.02906 ( 295) hydrogen bonds : angle 5.38772 ( 726) SS BOND : bond 0.00428 ( 24) SS BOND : angle 1.64715 ( 48) covalent geometry : bond 0.00248 (11145) covalent geometry : angle 0.57167 (15106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7005.24 seconds wall clock time: 127 minutes 14.85 seconds (7634.85 seconds total)