Starting phenix.real_space_refine on Tue May 13 18:11:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wbg_37424/05_2025/8wbg_37424_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wbg_37424/05_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_37424/05_2025/8wbg_37424.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wbg_37424/05_2025/8wbg_37424.map" model { file = "/net/cci-nas-00/data/ceres_data/8wbg_37424/05_2025/8wbg_37424_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wbg_37424/05_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-5687/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: 6.94, per 1000 atoms: 0.64 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: 2.75 Conformation dependent library (CDL) restraints added in 1.5 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: 1.14 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: 3.48 Time building geometry restraints manager: 3.25 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: 2.750 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: 0.470 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 27.570 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- 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 : 1.105 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: 0.2799 time to fit residues: 77.0409 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 : 1.128 ------------------------------------------------------------------------------- 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: 0.3674 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3674 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 1.285 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6530 (t0) cc_final: 0.6312 (t0) REVERT: A 97 MET cc_start: 0.8513 (mtm) cc_final: 0.8218 (mtt) REVERT: A 333 MET cc_start: 0.6269 (OUTLIER) cc_final: 0.5725 (mtp) REVERT: B 339 LYS cc_start: 0.7342 (pttm) cc_final: 0.6807 (ptmm) REVERT: a 69 ARG cc_start: 0.7134 (ptp-170) cc_final: 0.6735 (tpp80) REVERT: a 146 LYS cc_start: 0.8063 (mtpt) cc_final: 0.7802 (mmtt) REVERT: b 67 MET cc_start: 0.5872 (tmm) cc_final: 0.5580 (tmm) outliers start: 19 outliers final: 14 residues processed: 149 average time/residue: 0.2509 time to fit residues: 52.2402 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 : 1.273 ------------------------------------------------------------------------------- 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: 0.9980 chunk 93 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 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: 1.1182 ------------------------------------------------------------------------------- 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 = 0.4369 r_free = 0.4369 target = 0.209061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.168199 restraints weight = 12299.898| |-----------------------------------------------------------------------------| r_work (start): 0.3979 rms_B_bonded: 3.34 r_work: 0.3703 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.2097 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= 0.131 Angle : 0.590 11.497 15154 Z= 0.308 Chirality : 0.043 0.239 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.680 20.335 1476 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.32 % Favored : 95.61 % Rotamer: Outliers : 2.10 % Allowed : 9.59 % Favored : 88.31 % 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: 1.15 (0.42), residues: 159 sheet: -1.61 (0.31), residues: 293 loop : -0.75 (0.22), residues: 891 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 311 HIS 0.004 0.001 HIS b 254 PHE 0.021 0.002 PHE B 277 TYR 0.014 0.001 TYR A 331 ARG 0.004 0.000 ARG a 324 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 295) hydrogen bonds : angle 5.98277 ( 726) SS BOND : bond 0.00363 ( 24) SS BOND : angle 2.00199 ( 48) covalent geometry : bond 0.00318 (11145) covalent geometry : angle 0.58030 (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 159 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 1.113 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8557 (t0) cc_final: 0.8347 (t0) REVERT: A 97 MET cc_start: 0.8505 (mtm) cc_final: 0.8176 (mtt) REVERT: A 156 GLU cc_start: 0.7412 (pt0) cc_final: 0.7112 (pt0) REVERT: A 333 MET cc_start: 0.6388 (OUTLIER) cc_final: 0.5897 (mtp) REVERT: B 54 ILE cc_start: 0.6370 (mp) cc_final: 0.6149 (mp) REVERT: B 263 GLN cc_start: 0.7240 (mp10) cc_final: 0.6898 (mt0) REVERT: B 333 MET cc_start: 0.6750 (mtt) cc_final: 0.6293 (mtm) REVERT: B 339 LYS cc_start: 0.7303 (pttm) cc_final: 0.6897 (ptmm) REVERT: a 146 LYS cc_start: 0.8130 (mtpt) cc_final: 0.7861 (mmtt) REVERT: a 324 ARG cc_start: 0.8439 (mmt-90) cc_final: 0.8222 (mmt-90) REVERT: b 67 MET cc_start: 0.5892 (tmm) cc_final: 0.5600 (tmm) outliers start: 25 outliers final: 16 residues processed: 148 average time/residue: 0.2520 time to fit residues: 51.5243 Evaluate side-chains 131 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 114 time to evaluate : 1.207 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain A residue 333 MET 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 287 VAL Chi-restraints excluded: chain b residue 5 SER 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: 0.7980 chunk 85 optimal weight: 2.9990 chunk 11 optimal weight: 10.0000 chunk 111 optimal weight: 9.9990 chunk 106 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 chunk 78 optimal weight: 0.2980 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 254 HIS ** 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 = 0.4352 r_free = 0.4352 target = 0.207177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165826 restraints weight = 12268.008| |-----------------------------------------------------------------------------| r_work (start): 0.3953 rms_B_bonded: 3.23 r_work: 0.3689 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7551 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 11169 Z= 0.161 Angle : 0.610 14.279 15154 Z= 0.316 Chirality : 0.044 0.227 1584 Planarity : 0.004 0.041 1945 Dihedral : 4.689 18.176 1476 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 2.94 % Allowed : 10.43 % Favored : 86.63 % 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: -1.21 (0.23), residues: 1343 helix: 1.14 (0.42), residues: 159 sheet: -1.67 (0.32), residues: 289 loop : -0.86 (0.21), residues: 895 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.006 0.001 HIS b 254 PHE 0.019 0.002 PHE B 277 TYR 0.012 0.001 TYR A 331 ARG 0.005 0.000 ARG A 40 Details of bonding type rmsd hydrogen bonds : bond 0.03723 ( 295) hydrogen bonds : angle 6.00477 ( 726) SS BOND : bond 0.00472 ( 24) SS BOND : angle 1.93864 ( 48) covalent geometry : bond 0.00389 (11145) covalent geometry : angle 0.60142 (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 168 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 133 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8626 (t0) cc_final: 0.8404 (t0) REVERT: A 97 MET cc_start: 0.8425 (mtm) cc_final: 0.8086 (mtt) REVERT: A 156 GLU cc_start: 0.7449 (pt0) cc_final: 0.7146 (pt0) REVERT: B 339 LYS cc_start: 0.7429 (pttm) cc_final: 0.7051 (ptmm) REVERT: a 146 LYS cc_start: 0.8207 (mtpt) cc_final: 0.7957 (mmtt) REVERT: a 333 MET cc_start: 0.8152 (mmp) cc_final: 0.6972 (mmm) REVERT: b 67 MET cc_start: 0.5979 (tmm) cc_final: 0.5656 (tmm) outliers start: 35 outliers final: 24 residues processed: 156 average time/residue: 0.2340 time to fit residues: 51.6109 Evaluate side-chains 142 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 118 time to evaluate : 1.300 ------------------------------------------------------------------------------- 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 B residue 4 CYS 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 280 CYS 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 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 7 ASP 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 209 THR 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: 5.9990 chunk 35 optimal weight: 8.9990 chunk 13 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 115 optimal weight: 0.0050 chunk 50 optimal weight: 9.9990 chunk 57 optimal weight: 0.4980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 8.9990 chunk 128 optimal weight: 7.9990 overall best weight: 1.1998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN a 344 ASN b 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.208549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.167280 restraints weight = 12124.461| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 3.10 r_work: 0.3723 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.2574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 11169 Z= 0.133 Angle : 0.579 13.134 15154 Z= 0.300 Chirality : 0.043 0.214 1584 Planarity : 0.004 0.037 1945 Dihedral : 4.467 17.132 1476 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 2.78 % Allowed : 11.69 % Favored : 85.53 % 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 (0.23), residues: 1343 helix: 1.12 (0.42), residues: 159 sheet: -1.48 (0.32), residues: 287 loop : -0.92 (0.21), residues: 897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP b 68 HIS 0.004 0.001 HIS B 254 PHE 0.017 0.001 PHE B 277 TYR 0.012 0.001 TYR A 331 ARG 0.007 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03363 ( 295) hydrogen bonds : angle 5.78944 ( 726) SS BOND : bond 0.00439 ( 24) SS BOND : angle 1.85303 ( 48) covalent geometry : bond 0.00322 (11145) covalent geometry : angle 0.57078 (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 168 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 135 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8327 (tpp80) cc_final: 0.8001 (tpp80) REVERT: A 52 ASP cc_start: 0.6732 (t0) cc_final: 0.6523 (t0) REVERT: A 156 GLU cc_start: 0.7425 (pt0) cc_final: 0.7137 (pt0) REVERT: A 331 TYR cc_start: 0.6762 (OUTLIER) cc_final: 0.5086 (t80) REVERT: B 333 MET cc_start: 0.6671 (mtt) cc_final: 0.6197 (mtm) REVERT: B 339 LYS cc_start: 0.7669 (pttm) cc_final: 0.7371 (ptmm) REVERT: a 146 LYS cc_start: 0.8184 (mtpt) cc_final: 0.7947 (mmtt) REVERT: a 333 MET cc_start: 0.8174 (mmp) cc_final: 0.7193 (mmm) REVERT: b 67 MET cc_start: 0.5945 (tmm) cc_final: 0.5629 (tmm) REVERT: b 265 LYS cc_start: 0.6902 (mtpt) cc_final: 0.6584 (mtpt) outliers start: 33 outliers final: 26 residues processed: 157 average time/residue: 0.2459 time to fit residues: 53.6551 Evaluate side-chains 150 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 123 time to evaluate : 1.210 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS 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 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 7 ASP Chi-restraints excluded: chain b residue 13 THR 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 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 127 optimal weight: 0.0030 chunk 87 optimal weight: 4.9990 chunk 115 optimal weight: 6.9990 chunk 89 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 106 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 12 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 100 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 overall best weight: 1.1392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.208585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3999 r_free = 0.3999 target = 0.168059 restraints weight = 12255.647| |-----------------------------------------------------------------------------| r_work (start): 0.3978 rms_B_bonded: 3.39 r_work: 0.3708 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3708 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7522 moved from start: 0.2707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11169 Z= 0.129 Angle : 0.574 12.448 15154 Z= 0.297 Chirality : 0.043 0.205 1584 Planarity : 0.004 0.036 1945 Dihedral : 4.388 19.443 1476 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.29 % Favored : 94.56 % Rotamer: Outliers : 3.03 % Allowed : 12.87 % 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: -1.14 (0.23), residues: 1343 helix: 1.14 (0.42), residues: 159 sheet: -1.46 (0.33), residues: 273 loop : -0.88 (0.21), residues: 911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 68 HIS 0.004 0.001 HIS b 254 PHE 0.015 0.001 PHE B 277 TYR 0.010 0.001 TYR A 331 ARG 0.007 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03266 ( 295) hydrogen bonds : angle 5.67675 ( 726) SS BOND : bond 0.00441 ( 24) SS BOND : angle 1.82466 ( 48) covalent geometry : bond 0.00313 (11145) covalent geometry : angle 0.56594 (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: 36 poor density : 133 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.7113 (m-10) cc_final: 0.6820 (m-10) REVERT: A 52 ASP cc_start: 0.6812 (t0) cc_final: 0.6602 (t0) REVERT: A 156 GLU cc_start: 0.7444 (pt0) cc_final: 0.7127 (pt0) REVERT: A 331 TYR cc_start: 0.6778 (OUTLIER) cc_final: 0.5180 (t80) REVERT: B 54 ILE cc_start: 0.6294 (mp) cc_final: 0.6065 (mp) REVERT: B 141 LYS cc_start: 0.7530 (pptt) cc_final: 0.6803 (ttpp) REVERT: B 333 MET cc_start: 0.6682 (mtt) cc_final: 0.6271 (mtm) REVERT: B 339 LYS cc_start: 0.7750 (pttm) cc_final: 0.7466 (ptmm) REVERT: a 146 LYS cc_start: 0.8167 (mtpt) cc_final: 0.7931 (mmtt) REVERT: a 333 MET cc_start: 0.8161 (mmp) cc_final: 0.7846 (mmp) REVERT: b 265 LYS cc_start: 0.6875 (mtpt) cc_final: 0.6388 (mtpt) outliers start: 36 outliers final: 29 residues processed: 157 average time/residue: 0.2385 time to fit residues: 54.0253 Evaluate side-chains 155 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 125 time to evaluate : 1.085 ------------------------------------------------------------------------------- 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 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 331 TYR 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 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 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR 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 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: 2.9990 chunk 111 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 118 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 51 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 116 optimal weight: 20.0000 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.207007 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.165979 restraints weight = 12461.814| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 3.48 r_work: 0.3653 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7563 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11169 Z= 0.161 Angle : 0.597 11.795 15154 Z= 0.309 Chirality : 0.044 0.205 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.512 19.441 1476 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.18 % Favored : 93.67 % Rotamer: Outliers : 3.20 % Allowed : 13.04 % Favored : 83.77 % 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: -1.22 (0.23), residues: 1343 helix: 1.06 (0.41), residues: 159 sheet: -1.44 (0.33), residues: 271 loop : -0.96 (0.21), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 311 HIS 0.006 0.001 HIS B 269 PHE 0.015 0.002 PHE B 277 TYR 0.010 0.001 TYR A 331 ARG 0.004 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 295) hydrogen bonds : angle 5.76379 ( 726) SS BOND : bond 0.00432 ( 24) SS BOND : angle 1.93456 ( 48) covalent geometry : bond 0.00389 (11145) covalent geometry : angle 0.58813 (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 159 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 121 time to evaluate : 1.129 Fit side-chains revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8525 (t0) cc_final: 0.8303 (t0) REVERT: A 52 ASP cc_start: 0.6860 (t0) cc_final: 0.6635 (t0) REVERT: A 78 ILE cc_start: 0.6699 (mt) cc_final: 0.6387 (mt) REVERT: A 97 MET cc_start: 0.8485 (mtm) cc_final: 0.8141 (mtt) REVERT: A 156 GLU cc_start: 0.7468 (pt0) cc_final: 0.7143 (pt0) REVERT: A 331 TYR cc_start: 0.6907 (OUTLIER) cc_final: 0.5363 (t80) REVERT: B 141 LYS cc_start: 0.7536 (pptt) cc_final: 0.6832 (ttpp) REVERT: B 333 MET cc_start: 0.6706 (mtt) cc_final: 0.6255 (mtm) REVERT: B 339 LYS cc_start: 0.7782 (pttm) cc_final: 0.7484 (ptmm) REVERT: a 69 ARG cc_start: 0.7164 (ptp-170) cc_final: 0.6642 (tpp80) REVERT: a 146 LYS cc_start: 0.8239 (mtpt) cc_final: 0.7959 (mmtt) REVERT: b 67 MET cc_start: 0.5944 (tmm) cc_final: 0.5662 (tmm) outliers start: 38 outliers final: 31 residues processed: 147 average time/residue: 0.2223 time to fit residues: 46.7452 Evaluate side-chains 148 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 116 time to evaluate : 1.267 ------------------------------------------------------------------------------- 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 218 ILE Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 VAL 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 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 124 optimal weight: 0.2980 chunk 81 optimal weight: 8.9990 chunk 105 optimal weight: 3.9990 chunk 129 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 0.8980 overall best weight: 1.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.208765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167964 restraints weight = 12184.849| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.28 r_work: 0.3715 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11169 Z= 0.123 Angle : 0.572 11.378 15154 Z= 0.296 Chirality : 0.043 0.194 1584 Planarity : 0.003 0.035 1945 Dihedral : 4.338 17.647 1476 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.36 % Favored : 94.49 % Rotamer: Outliers : 3.28 % Allowed : 13.88 % Favored : 82.84 % 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: -1.16 (0.23), residues: 1343 helix: 1.07 (0.41), residues: 160 sheet: -1.41 (0.33), residues: 271 loop : -0.91 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 28 HIS 0.004 0.001 HIS b 254 PHE 0.016 0.001 PHE B 277 TYR 0.008 0.001 TYR A 331 ARG 0.004 0.000 ARG b 261 Details of bonding type rmsd hydrogen bonds : bond 0.03246 ( 295) hydrogen bonds : angle 5.60261 ( 726) SS BOND : bond 0.00400 ( 24) SS BOND : angle 1.84007 ( 48) covalent geometry : bond 0.00296 (11145) covalent geometry : angle 0.56295 (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 164 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 125 time to evaluate : 1.297 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6846 (t0) cc_final: 0.6642 (t0) REVERT: A 78 ILE cc_start: 0.6705 (mt) cc_final: 0.6397 (mt) REVERT: A 156 GLU cc_start: 0.7430 (pt0) cc_final: 0.7140 (pt0) REVERT: A 331 TYR cc_start: 0.6875 (OUTLIER) cc_final: 0.5410 (t80) REVERT: B 141 LYS cc_start: 0.7572 (pptt) cc_final: 0.6893 (ttpp) REVERT: B 333 MET cc_start: 0.6590 (mtt) cc_final: 0.6170 (mtm) REVERT: B 339 LYS cc_start: 0.7737 (pttm) cc_final: 0.7488 (ptmm) REVERT: a 69 ARG cc_start: 0.7125 (ptp-170) cc_final: 0.6611 (tpp80) REVERT: a 146 LYS cc_start: 0.8157 (mtpt) cc_final: 0.7933 (mmtt) REVERT: a 333 MET cc_start: 0.7828 (mmp) cc_final: 0.6787 (mmm) REVERT: b 67 MET cc_start: 0.5958 (tmm) cc_final: 0.5737 (tmm) REVERT: b 265 LYS cc_start: 0.6833 (mtpt) cc_final: 0.6385 (mtpt) outliers start: 39 outliers final: 33 residues processed: 151 average time/residue: 0.2315 time to fit residues: 49.9144 Evaluate side-chains 149 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 A residue 231 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN 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 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 a residue 350 VAL 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 15 CYS Chi-restraints excluded: chain b residue 17 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 134 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 50 optimal weight: 9.9990 chunk 48 optimal weight: 8.9990 chunk 114 optimal weight: 0.4980 chunk 61 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 73 optimal weight: 9.9990 chunk 133 optimal weight: 0.6980 chunk 100 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.208523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.167818 restraints weight = 12401.486| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 3.46 r_work: 0.3698 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.3698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 11169 Z= 0.133 Angle : 0.587 13.165 15154 Z= 0.300 Chirality : 0.043 0.181 1584 Planarity : 0.004 0.036 1945 Dihedral : 4.340 17.272 1476 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 3.20 % Allowed : 13.88 % Favored : 82.93 % 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: -1.22 (0.23), residues: 1343 helix: 1.10 (0.41), residues: 160 sheet: -1.53 (0.33), residues: 279 loop : -0.93 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP A 28 HIS 0.004 0.001 HIS b 254 PHE 0.015 0.002 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.004 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03327 ( 295) hydrogen bonds : angle 5.66126 ( 726) SS BOND : bond 0.00432 ( 24) SS BOND : angle 1.82797 ( 48) covalent geometry : bond 0.00322 (11145) covalent geometry : angle 0.57891 (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 154 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 116 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6920 (t0) cc_final: 0.6708 (t0) REVERT: A 78 ILE cc_start: 0.6756 (mt) cc_final: 0.6473 (mt) REVERT: A 156 GLU cc_start: 0.7459 (pt0) cc_final: 0.7168 (pt0) REVERT: A 324 ARG cc_start: 0.8377 (mmt90) cc_final: 0.7440 (mpt180) REVERT: A 331 TYR cc_start: 0.6904 (OUTLIER) cc_final: 0.5518 (t80) REVERT: B 141 LYS cc_start: 0.7565 (pptt) cc_final: 0.6897 (ttpp) REVERT: B 333 MET cc_start: 0.6618 (mtt) cc_final: 0.6196 (mtm) REVERT: a 69 ARG cc_start: 0.7143 (ptp-170) cc_final: 0.6626 (tpp80) REVERT: a 146 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7924 (mmtt) REVERT: a 310 GLU cc_start: 0.5494 (pm20) cc_final: 0.5266 (pm20) REVERT: a 333 MET cc_start: 0.7860 (mmp) cc_final: 0.6839 (mmm) REVERT: b 265 LYS cc_start: 0.6881 (mtpt) cc_final: 0.6483 (mtmt) REVERT: b 349 MET cc_start: 0.3133 (ptp) cc_final: 0.2818 (ptp) outliers start: 38 outliers final: 34 residues processed: 143 average time/residue: 0.2073 time to fit residues: 44.0937 Evaluate side-chains 146 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 A residue 231 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN 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 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 a residue 350 VAL 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 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 126 optimal weight: 9.9990 chunk 102 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 80 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 52 optimal weight: 0.9980 chunk 83 optimal weight: 6.9990 chunk 92 optimal weight: 0.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.209498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3993 r_free = 0.3993 target = 0.167753 restraints weight = 12213.995| |-----------------------------------------------------------------------------| r_work (start): 0.3977 rms_B_bonded: 3.45 r_work: 0.3690 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3690 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11169 Z= 0.118 Angle : 0.570 12.916 15154 Z= 0.293 Chirality : 0.042 0.174 1584 Planarity : 0.003 0.034 1945 Dihedral : 4.241 16.825 1476 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.36 % Favored : 94.49 % Rotamer: Outliers : 2.86 % Allowed : 14.21 % Favored : 82.93 % 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: -1.16 (0.23), residues: 1343 helix: 1.12 (0.41), residues: 160 sheet: -1.50 (0.32), residues: 279 loop : -0.88 (0.21), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP A 28 HIS 0.004 0.001 HIS b 254 PHE 0.014 0.001 PHE B 277 TYR 0.009 0.001 TYR A 331 ARG 0.004 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03168 ( 295) hydrogen bonds : angle 5.57200 ( 726) SS BOND : bond 0.00441 ( 24) SS BOND : angle 1.73139 ( 48) covalent geometry : bond 0.00283 (11145) covalent geometry : angle 0.56259 (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 149 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 115 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6995 (t0) cc_final: 0.6782 (t0) REVERT: A 78 ILE cc_start: 0.6408 (mt) cc_final: 0.6122 (mt) REVERT: A 156 GLU cc_start: 0.7404 (pt0) cc_final: 0.7083 (pt0) REVERT: A 331 TYR cc_start: 0.6959 (OUTLIER) cc_final: 0.5467 (t80) REVERT: B 141 LYS cc_start: 0.7553 (pptt) cc_final: 0.6936 (ttpp) REVERT: B 333 MET cc_start: 0.6365 (mtt) cc_final: 0.5912 (mtm) REVERT: a 69 ARG cc_start: 0.7117 (ptp-170) cc_final: 0.6466 (tpp80) REVERT: a 146 LYS cc_start: 0.8257 (mtpt) cc_final: 0.7912 (mmtt) REVERT: a 333 MET cc_start: 0.7925 (mmp) cc_final: 0.6903 (mmm) REVERT: b 349 MET cc_start: 0.3029 (ptp) cc_final: 0.2743 (ptp) outliers start: 34 outliers final: 32 residues processed: 138 average time/residue: 0.2200 time to fit residues: 44.3553 Evaluate side-chains 144 residues out of total 1189 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 111 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL 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 A residue 231 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 93 VAL Chi-restraints excluded: chain B residue 95 ASN 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 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP 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 a residue 350 VAL Chi-restraints excluded: chain b residue 9 SER 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 Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 84 optimal weight: 5.9990 chunk 122 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 127 optimal weight: 6.9990 chunk 86 optimal weight: 4.9990 chunk 111 optimal weight: 6.9990 chunk 38 optimal weight: 10.0000 chunk 22 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 chunk 74 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.206225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.164475 restraints weight = 12226.531| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 3.50 r_work: 0.3641 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11169 Z= 0.169 Angle : 0.619 13.344 15154 Z= 0.318 Chirality : 0.044 0.190 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.473 17.744 1476 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.63 % Favored : 93.22 % Rotamer: Outliers : 3.03 % Allowed : 14.38 % Favored : 82.59 % 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: -1.28 (0.23), residues: 1343 helix: 0.99 (0.41), residues: 160 sheet: -1.52 (0.31), residues: 299 loop : -0.96 (0.21), residues: 884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 28 HIS 0.006 0.001 HIS B 254 PHE 0.014 0.002 PHE B 277 TYR 0.010 0.001 TYR B 34 ARG 0.004 0.000 ARG B 29 Details of bonding type rmsd hydrogen bonds : bond 0.03614 ( 295) hydrogen bonds : angle 5.74804 ( 726) SS BOND : bond 0.00489 ( 24) SS BOND : angle 1.94752 ( 48) covalent geometry : bond 0.00409 (11145) covalent geometry : angle 0.60970 (15106) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5797.65 seconds wall clock time: 101 minutes 10.57 seconds (6070.57 seconds total)