Starting phenix.real_space_refine on Sun Jun 8 20:43:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.map" model { file = "/net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zba_39899/06_2025/8zba_39899.cif" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.035 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 84 5.16 5 C 6256 2.51 5 N 1718 2.21 5 O 1915 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 9973 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 313, 2453 Classifications: {'peptide': 313} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 18, 'TRANS': 294} Chain breaks: 2 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2493 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2493 Classifications: {'peptide': 317} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 298} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "a" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2518 Classifications: {'peptide': 319} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 300} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "b" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 318, 2509 Classifications: {'peptide': 318} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 299} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 6.83, per 1000 atoms: 0.68 Number of scatterers: 9973 At special positions: 0 Unit cell: (93.5, 106.25, 105.4, 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 84 16.00 O 1915 8.00 N 1718 7.00 C 6256 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=2.04 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 224 " 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=2.04 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 224 " 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 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 224 " 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 224 " 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: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2306 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 24 sheets defined 13.7% alpha, 14.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.30 Creating SS restraints... Processing helix chain 'A' and resid 40 through 52 Processing helix chain 'A' and resid 63 through 83 removed outlier: 5.158A pdb=" N ASP A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.131A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (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 227 through 231 removed outlier: 3.910A pdb=" N THR A 231 " --> pdb=" O LEU A 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 27 Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.660A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU B 52 " --> pdb=" O ALA B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 82 removed outlier: 5.199A pdb=" N ASP B 73 " --> pdb=" O ARG B 69 " (cutoff:3.500A) removed outlier: 5.234A pdb=" N GLU B 74 " --> pdb=" O SER B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 146 No H-bonds generated for 'chain 'B' and resid 144 through 146' Processing helix chain 'B' and resid 227 through 231 removed outlier: 3.952A pdb=" N THR B 231 " --> pdb=" O LEU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 249 removed outlier: 3.988A pdb=" N GLY B 249 " --> pdb=" O ARG B 245 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 removed outlier: 3.613A pdb=" N SER a 44 " --> pdb=" O VAL a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 82 removed outlier: 5.088A pdb=" N ASP a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 4.926A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) Processing helix chain 'a' and resid 227 through 231 removed outlier: 4.103A pdb=" N THR a 231 " --> pdb=" O LEU a 228 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 removed outlier: 3.568A pdb=" N LEU b 42 " --> pdb=" O ASP b 38 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA b 43 " --> pdb=" O PRO b 39 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N SER b 44 " --> pdb=" O VAL b 40 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N GLU b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N GLU b 52 " --> pdb=" O ALA b 48 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLY b 53 " --> pdb=" O SER b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 61 through 76 removed outlier: 4.718A pdb=" N ASP b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) Processing helix chain 'b' and resid 227 through 231 removed outlier: 3.986A pdb=" N THR b 231 " --> pdb=" O LEU b 228 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 13 through 15 removed outlier: 4.564A pdb=" N LYS A 14 " --> pdb=" O ALA A 5 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ALA A 5 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 5.110A pdb=" N GLN a 2 " --> pdb=" O ILE A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 34 through 35 removed outlier: 6.201A pdb=" N ARG A 166 " --> pdb=" O PHE A 158 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE A 158 " --> pdb=" O ARG A 166 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N TYR 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: 7.283A pdb=" N GLY A 56 " --> pdb=" O VAL 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 88 through 89 removed outlier: 3.563A pdb=" N VAL A 89 " --> pdb=" O PHE A 133 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 211 through 218 removed outlier: 6.453A pdb=" N GLY A 203 " --> pdb=" O HIS A 214 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N LEU A 216 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N TRP A 201 " --> pdb=" O LEU A 216 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N PHE A 200 " --> pdb=" O SER A 197 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LYS A 192 " --> pdb=" O ASN A 189 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLY a 185 " --> pdb=" O GLY a 196 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 275 through 277 Processing sheet with id=AA7, first strand: chain 'A' and resid 285 through 287 Processing sheet with id=AA8, first strand: chain 'B' and resid 12 through 15 removed outlier: 3.576A pdb=" N GLU B 12 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N LYS B 14 " --> pdb=" O ALA B 5 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 5 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN b 2 " --> pdb=" O ILE B 6 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 32 through 35 removed outlier: 3.783A pdb=" N SER B 33 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N VAL B 167 " --> pdb=" O SER B 33 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 56 through 57 removed outlier: 7.087A pdb=" N GLY B 56 " --> pdb=" O VAL B 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AB3, first strand: chain 'B' and resid 273 through 275 removed outlier: 4.440A pdb=" N LEU B 216 " --> pdb=" O VAL B 275 " (cutoff:3.500A) removed outlier: 5.336A pdb=" N ILE B 213 " --> pdb=" O HIS B 205 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N HIS B 205 " --> pdb=" O ILE B 213 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LYS B 192 " --> pdb=" O ASN B 189 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 312 through 313 Processing sheet with id=AB5, first strand: chain 'B' and resid 323 through 324 Processing sheet with id=AB6, first strand: chain 'a' and resid 56 through 57 removed outlier: 6.924A pdb=" N GLY a 56 " --> pdb=" O VAL a 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'a' and resid 86 through 87 Processing sheet with id=AB8, first strand: chain 'a' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'a' and resid 201 through 207 removed outlier: 6.667A pdb=" N TRP a 201 " --> pdb=" O LEU a 216 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N LEU a 216 " --> pdb=" O TRP a 201 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N GLY a 203 " --> pdb=" O HIS a 214 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ALA a 218 " --> pdb=" O LEU a 273 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'a' and resid 298 through 299 removed outlier: 3.901A pdb=" N THR a 298 " --> pdb=" O TYR a 331 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N TRP a 330 " --> pdb=" O PHE a 323 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 87 through 90 removed outlier: 6.902A pdb=" N SER b 87 " --> pdb=" O PHE b 133 " (cutoff:3.500A) removed outlier: 7.618A pdb=" N ILE b 135 " --> pdb=" O SER b 87 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N VAL b 89 " --> pdb=" O ILE b 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'b' and resid 195 through 197 removed outlier: 3.557A pdb=" N MET b 202 " --> pdb=" O HIS b 195 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE b 200 " --> pdb=" O SER b 197 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TRP b 201 " --> pdb=" O LEU b 216 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU b 216 " --> pdb=" O TRP b 201 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N GLY b 203 " --> pdb=" O HIS b 214 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'b' and resid 275 through 276 Processing sheet with id=AC5, first strand: chain 'b' and resid 286 through 287 removed outlier: 3.706A pdb=" N CYS b 313 " --> pdb=" O ILE b 286 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'b' and resid 298 through 299 removed outlier: 3.690A pdb=" N THR b 298 " --> pdb=" O TYR b 331 " (cutoff:3.500A) 198 hydrogen bonds defined for protein. 525 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: 2.65 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 3285 1.34 - 1.46: 2528 1.46 - 1.59: 4303 1.59 - 1.72: 0 1.72 - 1.84: 120 Bond restraints: 10236 Sorted by residual: bond pdb=" CA VAL a 167 " pdb=" C VAL a 167 " ideal model delta sigma weight residual 1.522 1.472 0.050 1.29e-02 6.01e+03 1.49e+01 bond pdb=" CA ARG A 166 " pdb=" C ARG A 166 " ideal model delta sigma weight residual 1.525 1.495 0.030 1.28e-02 6.10e+03 5.53e+00 bond pdb=" C VAL a 167 " pdb=" O VAL a 167 " ideal model delta sigma weight residual 1.237 1.213 0.024 1.09e-02 8.42e+03 5.04e+00 bond pdb=" N TYR a 168 " pdb=" CA TYR a 168 " ideal model delta sigma weight residual 1.456 1.431 0.025 1.14e-02 7.69e+03 4.78e+00 bond pdb=" CA VAL A 162 " pdb=" C VAL A 162 " ideal model delta sigma weight residual 1.523 1.495 0.028 1.27e-02 6.20e+03 4.76e+00 ... (remaining 10231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.59: 13480 1.59 - 3.19: 306 3.19 - 4.78: 59 4.78 - 6.37: 6 6.37 - 7.96: 2 Bond angle restraints: 13853 Sorted by residual: angle pdb=" N THR A 164 " pdb=" CA THR A 164 " pdb=" C THR A 164 " ideal model delta sigma weight residual 113.89 105.93 7.96 1.58e+00 4.01e-01 2.54e+01 angle pdb=" N ILE a 177 " pdb=" CA ILE a 177 " pdb=" C ILE a 177 " ideal model delta sigma weight residual 112.96 109.07 3.89 1.00e+00 1.00e+00 1.51e+01 angle pdb=" CA PRO a 103 " pdb=" C PRO a 103 " pdb=" N PHE a 104 " ideal model delta sigma weight residual 114.74 118.06 -3.32 1.03e+00 9.43e-01 1.04e+01 angle pdb=" C VAL A 162 " pdb=" CA VAL A 162 " pdb=" CB VAL A 162 " ideal model delta sigma weight residual 111.29 106.77 4.52 1.64e+00 3.72e-01 7.60e+00 angle pdb=" C ILE a 78 " pdb=" N PHE a 79 " pdb=" CA PHE a 79 " ideal model delta sigma weight residual 122.38 117.52 4.86 1.81e+00 3.05e-01 7.22e+00 ... (remaining 13848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 5466 17.47 - 34.94: 528 34.94 - 52.40: 87 52.40 - 69.87: 20 69.87 - 87.34: 14 Dihedral angle restraints: 6115 sinusoidal: 2519 harmonic: 3596 Sorted by residual: dihedral pdb=" CB CYS b 55 " pdb=" SG CYS b 55 " pdb=" SG CYS b 143 " pdb=" CB CYS b 143 " ideal model delta sinusoidal sigma weight residual -86.00 -173.34 87.34 1 1.00e+01 1.00e-02 9.15e+01 dihedral pdb=" CB CYS a 55 " pdb=" SG CYS a 55 " pdb=" SG CYS a 143 " pdb=" CB CYS a 143 " ideal model delta sinusoidal sigma weight residual 93.00 176.22 -83.22 1 1.00e+01 1.00e-02 8.47e+01 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 93.00 173.55 -80.55 1 1.00e+01 1.00e-02 8.02e+01 ... (remaining 6112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 887 0.034 - 0.067: 345 0.067 - 0.101: 133 0.101 - 0.135: 58 0.135 - 0.168: 8 Chirality restraints: 1431 Sorted by residual: chirality pdb=" CA MET a 318 " pdb=" N MET a 318 " pdb=" C MET a 318 " pdb=" CB MET a 318 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.08e-01 chirality pdb=" CA THR A 160 " pdb=" N THR A 160 " pdb=" C THR A 160 " pdb=" CB THR A 160 " both_signs ideal model delta sigma weight residual False 2.53 2.36 0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA ILE A 257 " pdb=" N ILE A 257 " pdb=" C ILE A 257 " pdb=" CB ILE A 257 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.01e-01 ... (remaining 1428 not shown) Planarity restraints: 1813 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 266 " 0.050 5.00e-02 4.00e+02 7.59e-02 9.22e+00 pdb=" N PRO A 267 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ARG B 314 " 0.012 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ARG B 314 " -0.040 2.00e-02 2.50e+03 pdb=" O ARG B 314 " 0.015 2.00e-02 2.50e+03 pdb=" N SER B 315 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 314 " -0.012 2.00e-02 2.50e+03 2.29e-02 5.25e+00 pdb=" C ARG A 314 " 0.040 2.00e-02 2.50e+03 pdb=" O ARG A 314 " -0.015 2.00e-02 2.50e+03 pdb=" N SER A 315 " -0.013 2.00e-02 2.50e+03 ... (remaining 1810 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 1750 2.77 - 3.30: 8918 3.30 - 3.83: 15167 3.83 - 4.37: 17335 4.37 - 4.90: 31228 Nonbonded interactions: 74398 Sorted by model distance: nonbonded pdb=" N ASP B 1 " pdb=" O ILE b 6 " model vdw 2.234 3.120 nonbonded pdb=" OG1 THR B 165 " pdb=" OE2 GLU b 12 " model vdw 2.250 3.040 nonbonded pdb=" OG SER B 87 " pdb=" O GLY B 131 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP A 38 " pdb=" N LYS A 41 " model vdw 2.269 3.120 nonbonded pdb=" OG SER B 304 " pdb=" NZ LYS B 306 " model vdw 2.271 3.120 ... (remaining 74393 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 108 or resid 130 through 139 or (resid 140 throu \ gh 141 and (name N or name CA or name C or name O or name CB )) or resid 142 thr \ ough 160 or resid 166 through 337)) selection = (chain 'B' and (resid 1 through 26 or resid 31 through 108 or resid 130 through \ 139 or (resid 140 through 141 and (name N or name CA or name C or name O or name \ CB )) or resid 142 through 160 or resid 166 through 337)) selection = (chain 'a' and (resid 1 through 26 or resid 31 through 108 or resid 130 through \ 140 or (resid 141 and (name N or name CA or name C or name O or name CB )) or re \ sid 142 through 337)) selection = (chain 'b' and (resid 1 through 26 or resid 31 through 140 or (resid 141 and (na \ me N or name CA or name C or name O or name CB )) or resid 142 through 337)) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.230 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: 0.390 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 25.330 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 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 0.050 10260 Z= 0.160 Angle : 0.600 7.963 13901 Z= 0.324 Chirality : 0.045 0.168 1431 Planarity : 0.005 0.076 1813 Dihedral : 13.820 86.434 3737 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.72 % Favored : 89.28 % Rotamer: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.46 (0.23), residues: 1241 helix: 1.33 (0.45), residues: 136 sheet: -3.00 (0.37), residues: 167 loop : -1.97 (0.20), residues: 938 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 150 HIS 0.004 0.001 HIS A 205 PHE 0.014 0.001 PHE a 104 TYR 0.013 0.001 TYR a 34 ARG 0.003 0.000 ARG a 245 Details of bonding type rmsd hydrogen bonds : bond 0.25586 ( 198) hydrogen bonds : angle 7.88340 ( 525) SS BOND : bond 0.00278 ( 24) SS BOND : angle 1.75238 ( 48) covalent geometry : bond 0.00318 (10236) covalent geometry : angle 0.59196 (13853) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 261 time to evaluate : 1.109 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6850 (tp30) cc_final: 0.6589 (tm-30) REVERT: A 71 ARG cc_start: 0.7897 (mmt90) cc_final: 0.6394 (mtt180) REVERT: A 94 LYS cc_start: 0.8004 (mmtt) cc_final: 0.7058 (pttt) REVERT: A 169 MET cc_start: 0.7967 (mtt) cc_final: 0.7762 (mtt) REVERT: A 235 SER cc_start: 0.6761 (m) cc_final: 0.6341 (p) REVERT: B 71 ARG cc_start: 0.7709 (mmt-90) cc_final: 0.4885 (tpt170) REVERT: B 92 ASP cc_start: 0.5949 (t70) cc_final: 0.5688 (t70) REVERT: B 168 TYR cc_start: 0.7694 (m-80) cc_final: 0.6868 (m-10) REVERT: B 176 THR cc_start: 0.8371 (m) cc_final: 0.8085 (p) REVERT: a 34 TYR cc_start: 0.6625 (m-80) cc_final: 0.6400 (m-80) REVERT: a 67 MET cc_start: 0.8186 (tmm) cc_final: 0.7745 (ttp) REVERT: a 79 PHE cc_start: 0.3626 (p90) cc_final: 0.3346 (p90) REVERT: b 12 GLU cc_start: 0.7190 (mm-30) cc_final: 0.5844 (mm-30) REVERT: b 158 PHE cc_start: 0.6881 (m-10) cc_final: 0.6384 (t80) REVERT: b 167 VAL cc_start: 0.5593 (m) cc_final: 0.5138 (t) REVERT: b 169 MET cc_start: 0.7066 (mmm) cc_final: 0.6522 (mmm) REVERT: b 177 ILE cc_start: 0.8503 (mp) cc_final: 0.8222 (tt) outliers start: 0 outliers final: 0 residues processed: 261 average time/residue: 0.2630 time to fit residues: 91.2617 Evaluate side-chains 170 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 9.9990 chunk 93 optimal weight: 0.6980 chunk 52 optimal weight: 0.8980 chunk 32 optimal weight: 4.9990 chunk 63 optimal weight: 0.9990 chunk 50 optimal weight: 6.9990 chunk 97 optimal weight: 8.9990 chunk 37 optimal weight: 2.9990 chunk 59 optimal weight: 0.0870 chunk 72 optimal weight: 0.9980 chunk 112 optimal weight: 0.7980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 ASN B 189 ASN B 265 ASN B 324 HIS a 76 ASN a 82 ASN a 290 ASN b 102 HIS b 290 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.225023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4218 r_free = 0.4218 target = 0.182615 restraints weight = 10588.906| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.176324 restraints weight = 15839.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.172486 restraints weight = 11888.303| |-----------------------------------------------------------------------------| r_work (final): 0.4076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7413 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10260 Z= 0.129 Angle : 0.621 9.284 13901 Z= 0.321 Chirality : 0.046 0.157 1431 Planarity : 0.005 0.052 1813 Dihedral : 4.349 18.683 1356 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 1.54 % Allowed : 10.33 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.57 (0.23), residues: 1241 helix: 1.09 (0.44), residues: 138 sheet: -2.97 (0.35), residues: 183 loop : -2.03 (0.20), residues: 920 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP a 311 HIS 0.004 0.001 HIS A 205 PHE 0.029 0.001 PHE a 79 TYR 0.012 0.001 TYR a 32 ARG 0.004 0.000 ARG a 69 Details of bonding type rmsd hydrogen bonds : bond 0.03588 ( 198) hydrogen bonds : angle 5.29024 ( 525) SS BOND : bond 0.00425 ( 24) SS BOND : angle 1.93676 ( 48) covalent geometry : bond 0.00318 (10236) covalent geometry : angle 0.61189 (13853) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 185 time to evaluate : 1.137 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8153 (mmt90) cc_final: 0.6645 (mtt180) REVERT: A 94 LYS cc_start: 0.7687 (mmtt) cc_final: 0.6934 (pttm) REVERT: A 136 ASP cc_start: 0.8283 (p0) cc_final: 0.8030 (p0) REVERT: A 235 SER cc_start: 0.6305 (m) cc_final: 0.6019 (p) REVERT: B 10 LYS cc_start: 0.7830 (tttp) cc_final: 0.7572 (tmtt) REVERT: B 71 ARG cc_start: 0.7347 (mmt-90) cc_final: 0.4744 (tpt170) REVERT: B 92 ASP cc_start: 0.5873 (t70) cc_final: 0.5585 (t70) REVERT: a 76 ASN cc_start: 0.6784 (m110) cc_final: 0.6566 (m110) REVERT: a 79 PHE cc_start: 0.3778 (p90) cc_final: 0.3282 (p90) REVERT: a 168 TYR cc_start: 0.7436 (m-80) cc_final: 0.7111 (m-80) REVERT: b 10 LYS cc_start: 0.6625 (tttm) cc_final: 0.5825 (tmtt) REVERT: b 12 GLU cc_start: 0.7241 (mm-30) cc_final: 0.5855 (mm-30) REVERT: b 158 PHE cc_start: 0.7013 (m-10) cc_final: 0.6365 (t80) outliers start: 17 outliers final: 9 residues processed: 194 average time/residue: 0.2334 time to fit residues: 63.3275 Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 159 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 284 SER Chi-restraints excluded: chain B residue 42 LEU Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 89 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 0 optimal weight: 7.9990 chunk 85 optimal weight: 0.8980 chunk 10 optimal weight: 6.9990 chunk 22 optimal weight: 0.3980 chunk 86 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 102 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN a 102 HIS b 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.224121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.166208 restraints weight = 10638.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.166786 restraints weight = 11821.483| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.169663 restraints weight = 9694.711| |-----------------------------------------------------------------------------| r_work (final): 0.4042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 10260 Z= 0.121 Angle : 0.591 9.089 13901 Z= 0.304 Chirality : 0.045 0.183 1431 Planarity : 0.005 0.052 1813 Dihedral : 4.261 17.833 1356 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 1.99 % Allowed : 12.86 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.23), residues: 1241 helix: 1.20 (0.45), residues: 139 sheet: -2.78 (0.37), residues: 173 loop : -2.04 (0.20), residues: 929 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 68 HIS 0.011 0.001 HIS B 214 PHE 0.027 0.001 PHE a 79 TYR 0.009 0.001 TYR B 260 ARG 0.009 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.03046 ( 198) hydrogen bonds : angle 4.92653 ( 525) SS BOND : bond 0.00390 ( 24) SS BOND : angle 1.73189 ( 48) covalent geometry : bond 0.00299 (10236) covalent geometry : angle 0.58351 (13853) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 170 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6590 (mm-30) cc_final: 0.6371 (tm-30) REVERT: A 71 ARG cc_start: 0.8159 (mmt90) cc_final: 0.6560 (mtt180) REVERT: A 94 LYS cc_start: 0.7901 (mmtt) cc_final: 0.6942 (pttm) REVERT: A 136 ASP cc_start: 0.8177 (p0) cc_final: 0.7929 (p0) REVERT: A 235 SER cc_start: 0.6869 (m) cc_final: 0.6419 (p) REVERT: B 10 LYS cc_start: 0.7680 (tttp) cc_final: 0.7369 (tmtt) REVERT: B 92 ASP cc_start: 0.5790 (t70) cc_final: 0.5509 (t70) REVERT: a 274 GLU cc_start: 0.7171 (tt0) cc_final: 0.6904 (mt-10) REVERT: a 286 ILE cc_start: 0.7634 (OUTLIER) cc_final: 0.7237 (pt) REVERT: b 10 LYS cc_start: 0.6523 (tttm) cc_final: 0.5706 (tttt) REVERT: b 12 GLU cc_start: 0.7240 (mm-30) cc_final: 0.5862 (mm-30) REVERT: b 158 PHE cc_start: 0.7025 (m-10) cc_final: 0.6385 (t80) outliers start: 22 outliers final: 13 residues processed: 181 average time/residue: 0.2071 time to fit residues: 53.7774 Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 155 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 298 THR Chi-restraints excluded: chain b residue 318 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 109 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 92 optimal weight: 0.8980 chunk 113 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 29 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 80 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN b 263 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4527 r_free = 0.4527 target = 0.221383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4119 r_free = 0.4119 target = 0.171682 restraints weight = 10567.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.163104 restraints weight = 12282.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.159867 restraints weight = 10153.464| |-----------------------------------------------------------------------------| r_work (final): 0.3967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.2829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10260 Z= 0.141 Angle : 0.598 7.952 13901 Z= 0.308 Chirality : 0.045 0.167 1431 Planarity : 0.005 0.050 1813 Dihedral : 4.346 18.235 1356 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.15 % Favored : 89.77 % Rotamer: Outliers : 2.54 % Allowed : 14.13 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.53 (0.23), residues: 1241 helix: 1.15 (0.45), residues: 141 sheet: -2.60 (0.36), residues: 185 loop : -2.09 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 330 HIS 0.010 0.001 HIS B 214 PHE 0.029 0.001 PHE a 79 TYR 0.011 0.001 TYR a 97 ARG 0.011 0.000 ARG B 11 Details of bonding type rmsd hydrogen bonds : bond 0.02971 ( 198) hydrogen bonds : angle 4.80401 ( 525) SS BOND : bond 0.00346 ( 24) SS BOND : angle 1.71450 ( 48) covalent geometry : bond 0.00343 (10236) covalent geometry : angle 0.59001 (13853) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6646 (mm-30) cc_final: 0.6377 (tm-30) REVERT: A 94 LYS cc_start: 0.7981 (mmtt) cc_final: 0.6996 (pttm) REVERT: A 136 ASP cc_start: 0.8263 (p0) cc_final: 0.8012 (p0) REVERT: B 10 LYS cc_start: 0.7578 (tttp) cc_final: 0.7182 (tmtt) REVERT: B 67 MET cc_start: 0.6183 (tpt) cc_final: 0.5856 (tpp) REVERT: B 92 ASP cc_start: 0.5930 (t70) cc_final: 0.5608 (t70) REVERT: a 76 ASN cc_start: 0.7171 (m110) cc_final: 0.6942 (m110) REVERT: a 336 ARG cc_start: 0.7519 (mmm-85) cc_final: 0.7103 (mtt90) REVERT: b 10 LYS cc_start: 0.6568 (tttm) cc_final: 0.5774 (tttt) REVERT: b 12 GLU cc_start: 0.7351 (mm-30) cc_final: 0.6113 (mm-30) REVERT: b 158 PHE cc_start: 0.6985 (m-10) cc_final: 0.6367 (t80) outliers start: 28 outliers final: 21 residues processed: 177 average time/residue: 0.2058 time to fit residues: 52.2524 Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 148 time to evaluate : 1.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 212 MET Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 89 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 180 ASP Chi-restraints excluded: chain b residue 298 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 96 optimal weight: 10.0000 chunk 81 optimal weight: 0.9990 chunk 101 optimal weight: 5.9990 chunk 112 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 92 optimal weight: 0.5980 chunk 5 optimal weight: 0.9980 chunk 117 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN a 82 ASN b 102 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4658 r_free = 0.4658 target = 0.231228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.188209 restraints weight = 10989.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.180200 restraints weight = 15555.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4195 r_free = 0.4195 target = 0.179462 restraints weight = 11525.912| |-----------------------------------------------------------------------------| r_work (final): 0.4181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 10260 Z= 0.126 Angle : 0.576 6.345 13901 Z= 0.297 Chirality : 0.044 0.149 1431 Planarity : 0.005 0.060 1813 Dihedral : 4.282 17.841 1356 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.19 % Favored : 90.73 % Rotamer: Outliers : 2.99 % Allowed : 16.39 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.50 (0.23), residues: 1241 helix: 1.13 (0.45), residues: 142 sheet: -2.51 (0.36), residues: 191 loop : -2.08 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 150 HIS 0.011 0.001 HIS B 214 PHE 0.029 0.001 PHE a 79 TYR 0.009 0.001 TYR a 97 ARG 0.007 0.001 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.02715 ( 198) hydrogen bonds : angle 4.76394 ( 525) SS BOND : bond 0.00324 ( 24) SS BOND : angle 1.57184 ( 48) covalent geometry : bond 0.00313 (10236) covalent geometry : angle 0.56960 (13853) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 157 time to evaluate : 1.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6560 (mm-30) cc_final: 0.6358 (tm-30) REVERT: A 71 ARG cc_start: 0.8214 (mmt90) cc_final: 0.6677 (mtt180) REVERT: A 94 LYS cc_start: 0.7749 (mmtt) cc_final: 0.6898 (pttm) REVERT: B 10 LYS cc_start: 0.7474 (tttp) cc_final: 0.7190 (tmtt) REVERT: B 67 MET cc_start: 0.6112 (tpt) cc_final: 0.5874 (tpp) REVERT: B 92 ASP cc_start: 0.5744 (t70) cc_final: 0.5424 (t70) REVERT: a 274 GLU cc_start: 0.6918 (tt0) cc_final: 0.6711 (mt-10) REVERT: b 10 LYS cc_start: 0.6598 (tttm) cc_final: 0.5965 (tttt) REVERT: b 12 GLU cc_start: 0.6975 (mm-30) cc_final: 0.5816 (mm-30) REVERT: b 158 PHE cc_start: 0.6923 (m-10) cc_final: 0.6471 (t80) outliers start: 33 outliers final: 24 residues processed: 174 average time/residue: 0.2109 time to fit residues: 53.0964 Evaluate side-chains 167 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 2 GLN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 146 SER Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain a residue 333 MET Chi-restraints excluded: chain b residue 42 LEU Chi-restraints excluded: chain b residue 45 ILE Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 180 ASP Chi-restraints excluded: chain b residue 298 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 56 optimal weight: 2.9990 chunk 83 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 69 optimal weight: 0.9980 chunk 41 optimal weight: 9.9990 chunk 93 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 6.9990 chunk 45 optimal weight: 9.9990 chunk 46 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN a 82 ASN a 195 HIS ** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN b 195 HIS b 256 HIS b 265 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.219705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.163736 restraints weight = 11215.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.162302 restraints weight = 13784.685| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.153231 restraints weight = 8965.498| |-----------------------------------------------------------------------------| r_work (final): 0.3953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.3565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.086 10260 Z= 0.292 Angle : 0.762 7.350 13901 Z= 0.401 Chirality : 0.049 0.183 1431 Planarity : 0.006 0.070 1813 Dihedral : 5.327 19.583 1356 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.62 % Favored : 86.30 % Rotamer: Outliers : 3.53 % Allowed : 17.75 % Favored : 78.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.23), residues: 1241 helix: 0.64 (0.44), residues: 148 sheet: -2.45 (0.37), residues: 183 loop : -2.40 (0.19), residues: 910 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 330 HIS 0.010 0.003 HIS B 214 PHE 0.042 0.002 PHE a 79 TYR 0.020 0.002 TYR a 34 ARG 0.012 0.001 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 198) hydrogen bonds : angle 5.27273 ( 525) SS BOND : bond 0.00445 ( 24) SS BOND : angle 1.94650 ( 48) covalent geometry : bond 0.00685 (10236) covalent geometry : angle 0.75507 (13853) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 188 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 149 time to evaluate : 1.177 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 LYS cc_start: 0.8104 (mmtt) cc_final: 0.6945 (pttm) REVERT: B 10 LYS cc_start: 0.7786 (tttp) cc_final: 0.7261 (tmtt) REVERT: B 67 MET cc_start: 0.6424 (tpt) cc_final: 0.6113 (tpp) REVERT: B 92 ASP cc_start: 0.5654 (t70) cc_final: 0.5275 (t70) REVERT: a 148 ARG cc_start: 0.7987 (mtt180) cc_final: 0.7765 (mtp85) REVERT: b 10 LYS cc_start: 0.6766 (tttm) cc_final: 0.5811 (tmtt) REVERT: b 12 GLU cc_start: 0.7289 (mm-30) cc_final: 0.5758 (mm-30) REVERT: b 35 TYR cc_start: 0.7061 (OUTLIER) cc_final: 0.6506 (m-10) REVERT: b 102 HIS cc_start: 0.7310 (OUTLIER) cc_final: 0.6942 (m90) REVERT: b 158 PHE cc_start: 0.7141 (m-10) cc_final: 0.6381 (t80) outliers start: 39 outliers final: 27 residues processed: 174 average time/residue: 0.2043 time to fit residues: 52.4313 Evaluate side-chains 173 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 144 time to evaluate : 1.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 6 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain A residue 317 THR Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 78 ILE Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 156 GLU Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain b residue 35 TYR Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 205 HIS Chi-restraints excluded: chain b residue 231 THR Chi-restraints excluded: chain b residue 298 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 29 optimal weight: 0.0670 chunk 101 optimal weight: 20.0000 chunk 59 optimal weight: 0.1980 chunk 118 optimal weight: 1.9990 chunk 73 optimal weight: 0.0010 chunk 94 optimal weight: 6.9990 chunk 106 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 57 optimal weight: 9.9990 chunk 77 optimal weight: 0.6980 chunk 122 optimal weight: 0.8980 overall best weight: 0.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN a 82 ASN b 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.220039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.173097 restraints weight = 10745.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.173512 restraints weight = 14541.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.173849 restraints weight = 10822.726| |-----------------------------------------------------------------------------| r_work (final): 0.4109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7298 moved from start: 0.3573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 10260 Z= 0.111 Angle : 0.589 8.681 13901 Z= 0.304 Chirality : 0.044 0.173 1431 Planarity : 0.005 0.059 1813 Dihedral : 4.448 21.140 1356 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.38 % Favored : 91.54 % Rotamer: Outliers : 2.26 % Allowed : 19.66 % Favored : 78.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.23), residues: 1241 helix: 1.33 (0.46), residues: 142 sheet: -2.71 (0.36), residues: 185 loop : -2.17 (0.19), residues: 914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP b 150 HIS 0.011 0.001 HIS B 214 PHE 0.041 0.001 PHE a 79 TYR 0.007 0.001 TYR b 34 ARG 0.005 0.000 ARG a 336 Details of bonding type rmsd hydrogen bonds : bond 0.02598 ( 198) hydrogen bonds : angle 4.77239 ( 525) SS BOND : bond 0.00307 ( 24) SS BOND : angle 1.41732 ( 48) covalent geometry : bond 0.00278 (10236) covalent geometry : angle 0.58382 (13853) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.6100 (tpt) cc_final: 0.5872 (tpp) REVERT: B 92 ASP cc_start: 0.5334 (t70) cc_final: 0.4943 (t70) REVERT: b 10 LYS cc_start: 0.6644 (tttm) cc_final: 0.6292 (tttt) REVERT: b 12 GLU cc_start: 0.6931 (mm-30) cc_final: 0.5648 (mm-30) REVERT: b 158 PHE cc_start: 0.6921 (m-10) cc_final: 0.6432 (t80) REVERT: b 255 ASN cc_start: 0.7306 (t0) cc_final: 0.7019 (t0) outliers start: 25 outliers final: 16 residues processed: 168 average time/residue: 0.1952 time to fit residues: 49.3245 Evaluate side-chains 153 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 137 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 176 THR Chi-restraints excluded: chain b residue 177 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 55 optimal weight: 0.0670 chunk 23 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 111 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 chunk 3 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 overall best weight: 0.8318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN b 91 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.215949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.181618 restraints weight = 10640.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.172080 restraints weight = 12756.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.165729 restraints weight = 14565.734| |-----------------------------------------------------------------------------| r_work (final): 0.4057 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7383 moved from start: 0.3652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 10260 Z= 0.130 Angle : 0.623 9.233 13901 Z= 0.320 Chirality : 0.045 0.216 1431 Planarity : 0.005 0.056 1813 Dihedral : 4.388 19.355 1356 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.91 % Favored : 90.01 % Rotamer: Outliers : 2.36 % Allowed : 20.02 % Favored : 77.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.55 (0.23), residues: 1241 helix: 1.45 (0.47), residues: 142 sheet: -2.65 (0.36), residues: 195 loop : -2.14 (0.20), residues: 904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 349 HIS 0.011 0.001 HIS B 214 PHE 0.039 0.001 PHE a 79 TYR 0.011 0.001 TYR a 34 ARG 0.004 0.000 ARG a 11 Details of bonding type rmsd hydrogen bonds : bond 0.02751 ( 198) hydrogen bonds : angle 4.81635 ( 525) SS BOND : bond 0.00337 ( 24) SS BOND : angle 1.86004 ( 48) covalent geometry : bond 0.00325 (10236) covalent geometry : angle 0.61401 (13853) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 143 time to evaluate : 1.036 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.6219 (tpt) cc_final: 0.5960 (tpp) REVERT: B 92 ASP cc_start: 0.5404 (t70) cc_final: 0.5007 (t70) REVERT: b 10 LYS cc_start: 0.6782 (tttm) cc_final: 0.6207 (tttt) REVERT: b 12 GLU cc_start: 0.6922 (mm-30) cc_final: 0.5688 (mm-30) REVERT: b 102 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6819 (m-70) REVERT: b 158 PHE cc_start: 0.6987 (m-10) cc_final: 0.6433 (t80) outliers start: 26 outliers final: 20 residues processed: 160 average time/residue: 0.1694 time to fit residues: 40.8416 Evaluate side-chains 160 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 139 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 156 GLU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 318 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 36 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 3.9990 chunk 9 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 114 optimal weight: 0.0870 chunk 39 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.3364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN ** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.213234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.177478 restraints weight = 10638.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.167760 restraints weight = 13575.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.163193 restraints weight = 14570.881| |-----------------------------------------------------------------------------| r_work (final): 0.4044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 10260 Z= 0.163 Angle : 0.654 9.892 13901 Z= 0.340 Chirality : 0.046 0.199 1431 Planarity : 0.005 0.057 1813 Dihedral : 4.584 19.452 1356 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 2.54 % Allowed : 20.65 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.23), residues: 1241 helix: 1.34 (0.46), residues: 142 sheet: -2.47 (0.36), residues: 201 loop : -2.17 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 330 HIS 0.011 0.001 HIS B 214 PHE 0.041 0.002 PHE a 79 TYR 0.012 0.001 TYR a 97 ARG 0.004 0.000 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.03040 ( 198) hydrogen bonds : angle 4.95299 ( 525) SS BOND : bond 0.00326 ( 24) SS BOND : angle 1.81060 ( 48) covalent geometry : bond 0.00399 (10236) covalent geometry : angle 0.64650 (13853) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 140 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 67 MET cc_start: 0.6300 (tpt) cc_final: 0.6018 (tpp) REVERT: B 92 ASP cc_start: 0.5368 (t70) cc_final: 0.4973 (t70) REVERT: b 10 LYS cc_start: 0.6934 (tttm) cc_final: 0.6416 (tttt) REVERT: b 12 GLU cc_start: 0.7096 (mm-30) cc_final: 0.5942 (mm-30) REVERT: b 102 HIS cc_start: 0.6982 (OUTLIER) cc_final: 0.6756 (m-70) REVERT: b 158 PHE cc_start: 0.7061 (m-10) cc_final: 0.6474 (t80) outliers start: 28 outliers final: 22 residues processed: 160 average time/residue: 0.1666 time to fit residues: 40.9073 Evaluate side-chains 157 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 134 time to evaluate : 1.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 172 VAL Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 231 THR Chi-restraints excluded: chain b residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 121 optimal weight: 0.0870 chunk 28 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 105 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.7760 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 270 GLN a 82 ASN a 265 ASN b 91 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.216108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.180387 restraints weight = 10765.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.170725 restraints weight = 13461.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4037 r_free = 0.4037 target = 0.166197 restraints weight = 14173.452| |-----------------------------------------------------------------------------| r_work (final): 0.4074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.3869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 10260 Z= 0.127 Angle : 0.625 9.478 13901 Z= 0.324 Chirality : 0.045 0.209 1431 Planarity : 0.005 0.052 1813 Dihedral : 4.437 19.751 1356 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.43 % Favored : 90.49 % Rotamer: Outliers : 2.17 % Allowed : 20.56 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.49 (0.23), residues: 1241 helix: 1.34 (0.46), residues: 142 sheet: -2.47 (0.36), residues: 201 loop : -2.11 (0.20), residues: 898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP b 150 HIS 0.011 0.001 HIS B 214 PHE 0.039 0.002 PHE a 79 TYR 0.009 0.001 TYR a 34 ARG 0.003 0.000 ARG a 336 Details of bonding type rmsd hydrogen bonds : bond 0.02747 ( 198) hydrogen bonds : angle 4.91879 ( 525) SS BOND : bond 0.00303 ( 24) SS BOND : angle 1.67855 ( 48) covalent geometry : bond 0.00320 (10236) covalent geometry : angle 0.61846 (13853) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2482 Ramachandran restraints generated. 1241 Oldfield, 0 Emsley, 1241 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 140 time to evaluate : 1.064 Fit side-chains revert: symmetry clash REVERT: B 67 MET cc_start: 0.6300 (tpt) cc_final: 0.6024 (tpp) REVERT: B 71 ARG cc_start: 0.7765 (mmp80) cc_final: 0.7497 (mmp80) REVERT: B 92 ASP cc_start: 0.5370 (t70) cc_final: 0.4992 (t70) REVERT: b 10 LYS cc_start: 0.6909 (tttm) cc_final: 0.6022 (tttt) REVERT: b 12 GLU cc_start: 0.7076 (mm-30) cc_final: 0.5944 (mm-30) REVERT: b 102 HIS cc_start: 0.7034 (OUTLIER) cc_final: 0.6746 (m-70) REVERT: b 158 PHE cc_start: 0.7097 (m-10) cc_final: 0.6484 (t80) outliers start: 24 outliers final: 21 residues processed: 156 average time/residue: 0.1746 time to fit residues: 42.0471 Evaluate side-chains 158 residues out of total 1109 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 136 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 CYS Chi-restraints excluded: chain A residue 75 ILE Chi-restraints excluded: chain A residue 154 GLN Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 316 CYS Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 44 SER Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain a residue 13 LEU Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 188 VAL Chi-restraints excluded: chain a residue 286 ILE Chi-restraints excluded: chain a residue 321 VAL Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 167 VAL Chi-restraints excluded: chain b residue 177 ILE Chi-restraints excluded: chain b residue 188 VAL Chi-restraints excluded: chain b residue 318 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 4 optimal weight: 6.9990 chunk 44 optimal weight: 8.9990 chunk 117 optimal weight: 0.0070 chunk 109 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 53 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 115 optimal weight: 2.9990 chunk 119 optimal weight: 30.0000 chunk 110 optimal weight: 0.8980 chunk 6 optimal weight: 7.9990 overall best weight: 1.1600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 255 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 82 ASN ** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.211122 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.149502 restraints weight = 10820.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.148658 restraints weight = 11967.021| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.150963 restraints weight = 10188.860| |-----------------------------------------------------------------------------| r_work (final): 0.3867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.3980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 10260 Z= 0.152 Angle : 0.649 10.076 13901 Z= 0.337 Chirality : 0.046 0.185 1431 Planarity : 0.005 0.050 1813 Dihedral : 4.517 19.585 1356 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.64 % Favored : 89.28 % Rotamer: Outliers : 2.63 % Allowed : 20.74 % Favored : 76.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.48 (0.23), residues: 1241 helix: 1.38 (0.47), residues: 142 sheet: -2.35 (0.37), residues: 191 loop : -2.15 (0.20), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 150 HIS 0.011 0.001 HIS B 214 PHE 0.025 0.002 PHE a 50 TYR 0.011 0.001 TYR a 97 ARG 0.004 0.000 ARG b 69 Details of bonding type rmsd hydrogen bonds : bond 0.02861 ( 198) hydrogen bonds : angle 4.97272 ( 525) SS BOND : bond 0.00313 ( 24) SS BOND : angle 1.69981 ( 48) covalent geometry : bond 0.00376 (10236) covalent geometry : angle 0.64270 (13853) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3524.14 seconds wall clock time: 63 minutes 45.97 seconds (3825.97 seconds total)