Starting phenix.real_space_refine on Wed Sep 25 08:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_39899.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_39899.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_39899.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_39899.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zba_39899/09_2024/8zba_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-5461/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: 6.73, per 1000 atoms: 0.67 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: 2.53 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: 1.13 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: 2.54 Time building geometry restraints manager: 2.97 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: 2.510 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: 0.070 Set scattering table: 0.090 Process input model: 25.010 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 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:2.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.590 ------------------------------------------------------------------------------- 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 10236 Z= 0.206 Angle : 0.592 7.963 13853 Z= 0.321 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 261 time to evaluate : 1.163 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: 0.2549 time to fit residues: 88.4437 Evaluate side-chains 170 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 10236 Z= 0.205 Angle : 0.612 9.284 13853 Z= 0.317 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 *********************** 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 fitting. rotamer outliers: 17 poor density : 185 time to evaluate : 1.093 Fit side-chains revert: symmetry clash REVERT: A 71 ARG cc_start: 0.8146 (mmt90) cc_final: 0.6530 (mtt180) REVERT: A 94 LYS cc_start: 0.7971 (mmtt) cc_final: 0.7006 (pttm) REVERT: A 136 ASP cc_start: 0.8223 (p0) cc_final: 0.7972 (p0) REVERT: A 235 SER cc_start: 0.6697 (m) cc_final: 0.6282 (p) REVERT: B 10 LYS cc_start: 0.7793 (tttp) cc_final: 0.7551 (tmtt) REVERT: B 71 ARG cc_start: 0.7344 (mmt-90) cc_final: 0.4757 (tpt170) REVERT: B 92 ASP cc_start: 0.5883 (t70) cc_final: 0.5599 (t70) REVERT: a 76 ASN cc_start: 0.7087 (m110) cc_final: 0.6760 (m110) REVERT: a 79 PHE cc_start: 0.3768 (p90) cc_final: 0.3243 (p90) REVERT: a 168 TYR cc_start: 0.7503 (m-80) cc_final: 0.7104 (m-80) REVERT: b 10 LYS cc_start: 0.6659 (tttm) cc_final: 0.5870 (tmtt) REVERT: b 12 GLU cc_start: 0.7240 (mm-30) cc_final: 0.5818 (mm-30) REVERT: b 158 PHE cc_start: 0.6942 (m-10) cc_final: 0.6401 (t80) outliers start: 17 outliers final: 9 residues processed: 194 average time/residue: 0.2313 time to fit residues: 63.2006 Evaluate side-chains 168 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 159 time to evaluate : 1.143 ------------------------------------------------------------------------------- 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 62 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 100 optimal weight: 8.9990 chunk 111 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 chunk 90 optimal weight: 0.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 10236 Z= 0.200 Angle : 0.588 8.834 13853 Z= 0.303 Chirality : 0.045 0.181 1431 Planarity : 0.005 0.052 1813 Dihedral : 4.299 17.875 1356 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.59 % Favored : 90.33 % Rotamer: Outliers : 1.90 % Allowed : 13.13 % Favored : 84.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.51 (0.23), residues: 1241 helix: 1.16 (0.45), residues: 140 sheet: -2.80 (0.37), residues: 173 loop : -2.05 (0.20), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 68 HIS 0.010 0.001 HIS B 214 PHE 0.028 0.001 PHE a 79 TYR 0.010 0.001 TYR B 260 ARG 0.014 0.001 ARG B 11 *********************** 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 190 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 169 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6662 (mm-30) cc_final: 0.6392 (tm-30) REVERT: A 71 ARG cc_start: 0.8142 (mmt90) cc_final: 0.6508 (mtt180) REVERT: A 94 LYS cc_start: 0.8032 (mmtt) cc_final: 0.6984 (pttm) REVERT: A 136 ASP cc_start: 0.8167 (p0) cc_final: 0.7922 (p0) REVERT: A 235 SER cc_start: 0.6831 (m) cc_final: 0.6385 (p) REVERT: B 10 LYS cc_start: 0.7659 (tttp) cc_final: 0.7327 (tmtt) REVERT: B 92 ASP cc_start: 0.5803 (t70) cc_final: 0.5496 (t70) REVERT: a 274 GLU cc_start: 0.7183 (tt0) cc_final: 0.6909 (mt-10) REVERT: a 286 ILE cc_start: 0.7648 (OUTLIER) cc_final: 0.7214 (pt) REVERT: a 336 ARG cc_start: 0.7469 (mmm-85) cc_final: 0.7011 (mtt90) REVERT: b 10 LYS cc_start: 0.6570 (tttm) cc_final: 0.5752 (tttt) REVERT: b 12 GLU cc_start: 0.7237 (mm-30) cc_final: 0.5830 (mm-30) REVERT: b 158 PHE cc_start: 0.7026 (m-10) cc_final: 0.6424 (t80) outliers start: 21 outliers final: 11 residues processed: 180 average time/residue: 0.2094 time to fit residues: 53.3369 Evaluate side-chains 165 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 153 time to evaluate : 1.094 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 111 optimal weight: 0.7980 chunk 84 optimal weight: 4.9990 chunk 58 optimal weight: 10.0000 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 119 optimal weight: 10.0000 chunk 59 optimal weight: 0.0770 chunk 107 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 overall best weight: 1.2940 ------------------------------------------------------------------------------- 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 b 265 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10236 Z= 0.248 Angle : 0.605 8.041 13853 Z= 0.313 Chirality : 0.045 0.164 1431 Planarity : 0.005 0.050 1813 Dihedral : 4.448 18.107 1356 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.64 % Favored : 89.28 % Rotamer: Outliers : 2.81 % Allowed : 14.67 % Favored : 82.52 % 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: 1.11 (0.45), residues: 141 sheet: -2.58 (0.37), residues: 185 loop : -2.12 (0.20), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 330 HIS 0.010 0.001 HIS B 214 PHE 0.029 0.002 PHE a 79 TYR 0.011 0.001 TYR a 97 ARG 0.008 0.000 ARG B 11 *********************** 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 fitting. rotamer outliers: 31 poor density : 160 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6760 (mm-30) cc_final: 0.6432 (tm-30) REVERT: A 94 LYS cc_start: 0.8110 (mmtt) cc_final: 0.7039 (pttm) REVERT: B 67 MET cc_start: 0.6169 (tpt) cc_final: 0.5871 (tpp) REVERT: B 71 ARG cc_start: 0.7948 (mmp80) cc_final: 0.7744 (mmt-90) REVERT: B 92 ASP cc_start: 0.5755 (t70) cc_final: 0.5438 (t70) REVERT: a 76 ASN cc_start: 0.7117 (m110) cc_final: 0.6887 (m110) REVERT: a 336 ARG cc_start: 0.7465 (mmm-85) cc_final: 0.7019 (mtt90) REVERT: b 10 LYS cc_start: 0.6658 (tttm) cc_final: 0.5893 (tttt) REVERT: b 12 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6008 (mm-30) REVERT: b 158 PHE cc_start: 0.7001 (m-10) cc_final: 0.6478 (t80) outliers start: 31 outliers final: 22 residues processed: 179 average time/residue: 0.2101 time to fit residues: 53.1934 Evaluate side-chains 167 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 307 VAL Chi-restraints excluded: chain A residue 315 SER Chi-restraints excluded: chain A residue 316 CYS 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 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 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 99 optimal weight: 6.9990 chunk 68 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 chunk 107 optimal weight: 6.9990 chunk 30 optimal weight: 0.0770 overall best weight: 1.0742 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7449 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10236 Z= 0.230 Angle : 0.592 6.753 13853 Z= 0.306 Chirality : 0.045 0.154 1431 Planarity : 0.005 0.054 1813 Dihedral : 4.413 17.660 1356 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.07 % Favored : 89.85 % Rotamer: Outliers : 3.26 % Allowed : 17.21 % Favored : 79.53 % 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: -2.56 (0.23), residues: 1241 helix: 1.12 (0.45), residues: 141 sheet: -2.53 (0.36), residues: 185 loop : -2.14 (0.20), residues: 915 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 0.030 0.001 PHE a 79 TYR 0.010 0.001 TYR a 97 ARG 0.006 0.000 ARG b 69 *********************** 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 192 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 156 time to evaluate : 1.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6788 (mm-30) cc_final: 0.6451 (tm-30) REVERT: A 94 LYS cc_start: 0.7798 (mmtt) cc_final: 0.6749 (pttm) REVERT: B 67 MET cc_start: 0.6158 (tpt) cc_final: 0.5829 (tpp) REVERT: B 92 ASP cc_start: 0.5731 (t70) cc_final: 0.5397 (t70) REVERT: a 76 ASN cc_start: 0.7054 (m110) cc_final: 0.6805 (m110) REVERT: a 274 GLU cc_start: 0.7190 (tt0) cc_final: 0.6916 (mt-10) REVERT: a 336 ARG cc_start: 0.7459 (mmm-85) cc_final: 0.7041 (mtt90) REVERT: b 10 LYS cc_start: 0.6659 (tttm) cc_final: 0.6008 (tttt) REVERT: b 12 GLU cc_start: 0.7287 (mm-30) cc_final: 0.5908 (mm-30) REVERT: b 158 PHE cc_start: 0.6976 (m-10) cc_final: 0.6439 (t80) outliers start: 36 outliers final: 25 residues processed: 176 average time/residue: 0.1926 time to fit residues: 49.4393 Evaluate side-chains 166 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 141 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 177 ILE Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain B residue 239 SER Chi-restraints excluded: chain a residue 2 GLN 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 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 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 40 optimal weight: 5.9990 chunk 107 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 29 optimal weight: 0.7980 chunk 119 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 55 optimal weight: 0.0050 chunk 9 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 62 optimal weight: 7.9990 overall best weight: 2.5198 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.3478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.077 10236 Z= 0.411 Angle : 0.718 6.826 13853 Z= 0.377 Chirality : 0.048 0.170 1431 Planarity : 0.006 0.075 1813 Dihedral : 5.107 18.709 1356 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.08 % Allowed : 13.22 % Favored : 86.70 % Rotamer: Outliers : 3.62 % Allowed : 17.84 % Favored : 78.53 % 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: -2.81 (0.23), residues: 1241 helix: 0.79 (0.44), residues: 148 sheet: -2.43 (0.37), residues: 178 loop : -2.39 (0.19), residues: 915 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 330 HIS 0.010 0.002 HIS B 214 PHE 0.046 0.002 PHE B 79 TYR 0.017 0.002 TYR a 34 ARG 0.008 0.001 ARG b 69 *********************** 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 189 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 149 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6558 (tm-30) REVERT: B 67 MET cc_start: 0.6461 (tpt) cc_final: 0.6194 (tpp) REVERT: B 92 ASP cc_start: 0.5683 (t70) cc_final: 0.5322 (t70) REVERT: a 13 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8331 (tt) REVERT: a 66 GLU cc_start: 0.8221 (tm-30) cc_final: 0.8005 (tm-30) REVERT: a 76 ASN cc_start: 0.7057 (m110) cc_final: 0.6744 (m110) REVERT: a 336 ARG cc_start: 0.7489 (mmm-85) cc_final: 0.7100 (mtt90) REVERT: b 10 LYS cc_start: 0.6864 (tttm) cc_final: 0.6183 (tttt) REVERT: b 12 GLU cc_start: 0.7210 (mm-30) cc_final: 0.5924 (mm-30) REVERT: b 35 TYR cc_start: 0.7083 (OUTLIER) cc_final: 0.6484 (m-10) REVERT: b 102 HIS cc_start: 0.7259 (OUTLIER) cc_final: 0.6963 (m90) REVERT: b 158 PHE cc_start: 0.7099 (m-10) cc_final: 0.6424 (t80) outliers start: 40 outliers final: 30 residues processed: 176 average time/residue: 0.1745 time to fit residues: 46.1172 Evaluate side-chains 176 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 143 time to evaluate : 1.154 ------------------------------------------------------------------------------- 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 73 ASP 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 13 LEU Chi-restraints excluded: chain a residue 29 LEU Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 149 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 a residue 333 MET 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 180 ASP 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 115 optimal weight: 0.7980 chunk 13 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 119 optimal weight: 7.9990 chunk 74 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 55 optimal weight: 0.4980 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 10236 Z= 0.209 Angle : 0.600 7.254 13853 Z= 0.311 Chirality : 0.045 0.161 1431 Planarity : 0.005 0.062 1813 Dihedral : 4.560 19.792 1356 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.08 % Allowed : 9.27 % Favored : 90.65 % Rotamer: Outliers : 3.17 % Allowed : 19.75 % Favored : 77.08 % 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: -2.61 (0.23), residues: 1241 helix: 1.39 (0.46), residues: 140 sheet: -2.51 (0.37), residues: 183 loop : -2.25 (0.19), residues: 918 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 226 HIS 0.011 0.001 HIS B 214 PHE 0.051 0.002 PHE B 79 TYR 0.009 0.001 TYR b 34 ARG 0.005 0.000 ARG B 69 *********************** 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 185 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 150 time to evaluate : 1.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6810 (mm-30) cc_final: 0.6449 (tm-30) REVERT: B 67 MET cc_start: 0.6329 (tpt) cc_final: 0.6021 (tpp) REVERT: B 71 ARG cc_start: 0.7737 (mmp80) cc_final: 0.7484 (mmp80) REVERT: B 92 ASP cc_start: 0.5662 (t70) cc_final: 0.5264 (t70) REVERT: a 13 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8362 (tt) REVERT: a 66 GLU cc_start: 0.8128 (tm-30) cc_final: 0.7831 (tm-30) REVERT: a 336 ARG cc_start: 0.7480 (mmm-85) cc_final: 0.7098 (mtt90) REVERT: b 10 LYS cc_start: 0.6743 (tttm) cc_final: 0.6258 (tttt) REVERT: b 12 GLU cc_start: 0.7187 (mm-30) cc_final: 0.5714 (mm-30) REVERT: b 102 HIS cc_start: 0.7271 (OUTLIER) cc_final: 0.6933 (m90) REVERT: b 136 ASP cc_start: 0.6711 (OUTLIER) cc_final: 0.6477 (m-30) REVERT: b 158 PHE cc_start: 0.7099 (m-10) cc_final: 0.6431 (t80) REVERT: b 174 GLU cc_start: 0.7978 (pp20) cc_final: 0.7312 (pp20) outliers start: 35 outliers final: 27 residues processed: 173 average time/residue: 0.1691 time to fit residues: 44.0861 Evaluate side-chains 173 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 143 time to evaluate : 1.059 ------------------------------------------------------------------------------- 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 134 ILE 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 132 SER 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 82 ASN 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 a residue 333 MET Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 136 ASP 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 205 HIS Chi-restraints excluded: chain b residue 231 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 73 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 71 optimal weight: 0.9990 chunk 36 optimal weight: 9.9990 chunk 23 optimal weight: 0.9980 chunk 75 optimal weight: 3.9990 chunk 81 optimal weight: 0.8980 chunk 59 optimal weight: 9.9990 chunk 11 optimal weight: 0.0170 chunk 93 optimal weight: 10.0000 chunk 108 optimal weight: 1.9990 overall best weight: 0.7620 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7451 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10236 Z= 0.205 Angle : 0.606 9.631 13853 Z= 0.313 Chirality : 0.045 0.146 1431 Planarity : 0.005 0.058 1813 Dihedral : 4.447 20.192 1356 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.15 % Favored : 89.77 % Rotamer: Outliers : 3.26 % Allowed : 20.20 % Favored : 76.54 % 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: 1.42 (0.47), residues: 140 sheet: -2.46 (0.37), residues: 188 loop : -2.19 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 68 HIS 0.011 0.001 HIS B 214 PHE 0.051 0.001 PHE B 79 TYR 0.010 0.001 TYR a 97 ARG 0.004 0.000 ARG B 69 *********************** 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 189 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 153 time to evaluate : 1.334 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6773 (mm-30) cc_final: 0.6429 (tm-30) REVERT: B 67 MET cc_start: 0.6297 (tpt) cc_final: 0.6024 (tpp) REVERT: B 71 ARG cc_start: 0.7704 (mmp80) cc_final: 0.7396 (mmp80) REVERT: B 92 ASP cc_start: 0.5643 (t70) cc_final: 0.5220 (t70) REVERT: a 13 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8376 (tt) REVERT: a 66 GLU cc_start: 0.8094 (tm-30) cc_final: 0.7794 (tm-30) REVERT: a 336 ARG cc_start: 0.7483 (mmm-85) cc_final: 0.7114 (mtt90) REVERT: b 10 LYS cc_start: 0.6758 (tttm) cc_final: 0.6293 (tttt) REVERT: b 12 GLU cc_start: 0.7154 (mm-30) cc_final: 0.5788 (mm-30) REVERT: b 102 HIS cc_start: 0.7326 (OUTLIER) cc_final: 0.6975 (m90) REVERT: b 136 ASP cc_start: 0.6775 (OUTLIER) cc_final: 0.6514 (m-30) REVERT: b 158 PHE cc_start: 0.7153 (m-10) cc_final: 0.6445 (t80) outliers start: 36 outliers final: 30 residues processed: 176 average time/residue: 0.1882 time to fit residues: 49.6975 Evaluate side-chains 175 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 142 time to evaluate : 1.203 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain A residue 264 THR 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 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 82 ASN Chi-restraints excluded: chain a residue 88 VAL Chi-restraints excluded: chain a residue 102 HIS Chi-restraints excluded: chain a residue 146 SER 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 a residue 333 MET Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 136 ASP 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 205 HIS Chi-restraints excluded: chain b residue 231 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 114 optimal weight: 0.0980 chunk 104 optimal weight: 0.4980 chunk 111 optimal weight: 3.9990 chunk 67 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 87 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 100 optimal weight: 7.9990 chunk 105 optimal weight: 4.9990 chunk 110 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 82 ASN a 265 ASN b 91 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 10236 Z= 0.198 Angle : 0.597 7.716 13853 Z= 0.309 Chirality : 0.045 0.142 1431 Planarity : 0.005 0.054 1813 Dihedral : 4.372 20.024 1356 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.08 % Allowed : 8.94 % Favored : 90.98 % Rotamer: Outliers : 3.08 % Allowed : 20.65 % Favored : 76.27 % 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: 1.40 (0.46), residues: 142 sheet: -2.29 (0.37), residues: 186 loop : -2.18 (0.19), residues: 913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP b 68 HIS 0.011 0.001 HIS B 214 PHE 0.052 0.002 PHE B 79 TYR 0.009 0.001 TYR b 34 ARG 0.009 0.000 ARG B 11 *********************** 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 183 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 149 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6755 (mm-30) cc_final: 0.6408 (tm-30) REVERT: B 10 LYS cc_start: 0.7538 (tttp) cc_final: 0.7086 (tmtt) REVERT: B 67 MET cc_start: 0.6290 (tpt) cc_final: 0.5982 (tpp) REVERT: B 71 ARG cc_start: 0.7680 (mmp80) cc_final: 0.7383 (mmp80) REVERT: B 92 ASP cc_start: 0.5617 (t70) cc_final: 0.5199 (t70) REVERT: a 13 LEU cc_start: 0.8641 (OUTLIER) cc_final: 0.8371 (tt) REVERT: a 66 GLU cc_start: 0.8087 (tm-30) cc_final: 0.7776 (tm-30) REVERT: a 336 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7185 (mtt90) REVERT: b 10 LYS cc_start: 0.6760 (tttm) cc_final: 0.6294 (tttt) REVERT: b 12 GLU cc_start: 0.7123 (mm-30) cc_final: 0.5779 (mm-30) REVERT: b 102 HIS cc_start: 0.7309 (OUTLIER) cc_final: 0.6934 (m90) REVERT: b 136 ASP cc_start: 0.6713 (OUTLIER) cc_final: 0.6470 (m-30) REVERT: b 158 PHE cc_start: 0.7144 (m-10) cc_final: 0.6453 (t80) outliers start: 34 outliers final: 28 residues processed: 174 average time/residue: 0.1780 time to fit residues: 46.5353 Evaluate side-chains 172 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 141 time to evaluate : 1.122 ------------------------------------------------------------------------------- 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 134 ILE 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 132 SER Chi-restraints excluded: chain B residue 177 ILE 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 146 SER 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 a residue 333 MET Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 136 ASP 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 205 HIS Chi-restraints excluded: chain b residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 117 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 81 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 98 optimal weight: 0.9990 chunk 10 optimal weight: 4.9990 chunk 75 optimal weight: 0.5980 chunk 60 optimal weight: 0.3980 chunk 78 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 270 GLN a 76 ASN a 82 ASN ** a 205 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 91 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7456 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 10236 Z= 0.220 Angle : 0.608 8.422 13853 Z= 0.316 Chirality : 0.045 0.146 1431 Planarity : 0.005 0.054 1813 Dihedral : 4.411 19.212 1356 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.23 % Favored : 89.69 % Rotamer: Outliers : 3.08 % Allowed : 20.74 % Favored : 76.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.32 (0.46), residues: 143 sheet: -2.31 (0.37), residues: 186 loop : -2.17 (0.20), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP b 68 HIS 0.011 0.001 HIS B 214 PHE 0.052 0.002 PHE B 79 TYR 0.009 0.001 TYR a 97 ARG 0.004 0.000 ARG B 11 ********************** 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 181 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 147 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.6781 (tm-30) cc_final: 0.6434 (tm-30) REVERT: B 10 LYS cc_start: 0.7555 (tttp) cc_final: 0.7162 (tmtt) REVERT: B 67 MET cc_start: 0.6275 (tpt) cc_final: 0.6046 (tpp) REVERT: B 92 ASP cc_start: 0.5607 (t70) cc_final: 0.5185 (t70) REVERT: a 13 LEU cc_start: 0.8602 (OUTLIER) cc_final: 0.8334 (tt) REVERT: a 66 GLU cc_start: 0.8098 (tm-30) cc_final: 0.7791 (tm-30) REVERT: a 336 ARG cc_start: 0.7506 (mmm-85) cc_final: 0.7205 (mtt90) REVERT: b 10 LYS cc_start: 0.6785 (tttm) cc_final: 0.6270 (tttt) REVERT: b 12 GLU cc_start: 0.7184 (mm-30) cc_final: 0.5921 (mm-30) REVERT: b 102 HIS cc_start: 0.7329 (OUTLIER) cc_final: 0.6901 (m-70) REVERT: b 136 ASP cc_start: 0.6727 (OUTLIER) cc_final: 0.6493 (m-30) REVERT: b 158 PHE cc_start: 0.7141 (m-10) cc_final: 0.6457 (t80) outliers start: 34 outliers final: 29 residues processed: 170 average time/residue: 0.1805 time to fit residues: 45.9414 Evaluate side-chains 173 residues out of total 1109 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 141 time to evaluate : 1.125 ------------------------------------------------------------------------------- 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 134 ILE Chi-restraints excluded: chain A residue 264 THR 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 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 146 SER 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 a residue 333 MET Chi-restraints excluded: chain b residue 57 LEU Chi-restraints excluded: chain b residue 102 HIS Chi-restraints excluded: chain b residue 136 ASP 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 188 VAL Chi-restraints excluded: chain b residue 205 HIS Chi-restraints excluded: chain b residue 231 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 124 random chunks: chunk 104 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 27 optimal weight: 0.9990 chunk 98 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 101 optimal weight: 1.9990 chunk 12 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 86 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 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 = 0.4431 r_free = 0.4431 target = 0.210586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.142033 restraints weight = 10773.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.143690 restraints weight = 8699.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.145198 restraints weight = 7389.128| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 10236 Z= 0.265 Angle : 0.633 7.905 13853 Z= 0.330 Chirality : 0.046 0.149 1431 Planarity : 0.005 0.051 1813 Dihedral : 4.589 19.228 1356 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.08 % Allowed : 10.96 % Favored : 88.96 % Rotamer: Outliers : 3.17 % Allowed : 21.29 % Favored : 75.54 % 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: -2.51 (0.23), residues: 1241 helix: 1.31 (0.46), residues: 141 sheet: -2.31 (0.36), residues: 191 loop : -2.17 (0.20), residues: 909 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 0.053 0.002 PHE B 79 TYR 0.011 0.001 TYR a 97 ARG 0.004 0.000 ARG B 11 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2160.00 seconds wall clock time: 39 minutes 21.32 seconds (2361.32 seconds total)