Starting phenix.real_space_refine on Sun Aug 4 15:49:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8wbg_37424/08_2024/8wbg_37424_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 6811 2.51 5 N 1947 2.21 5 O 2016 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "a ASP 208": "OD1" <-> "OD2" Residue "a GLU 237": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 10854 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 352, 2819 Classifications: {'peptide': 352} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 332} Chain: "B" Number of atoms: 2759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2759 Classifications: {'peptide': 345} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 325} Chain breaks: 1 Chain: "a" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Chain: "b" Number of atoms: 2638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 330, 2638 Classifications: {'peptide': 330} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 311} Chain breaks: 1 Time building chain proxies: 6.52, per 1000 atoms: 0.60 Number of scatterers: 10854 At special positions: 0 Unit cell: (109.65, 121.55, 111.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2016 8.00 N 1947 7.00 C 6811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=24, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 15 " distance=2.03 Simple disulfide: pdb=" SG CYS A 55 " - pdb=" SG CYS A 143 " distance=2.03 Simple disulfide: pdb=" SG CYS A 179 " - pdb=" SG CYS A 223 " distance=2.03 Simple disulfide: pdb=" SG CYS A 280 " - pdb=" SG CYS A 329 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 312 " distance=2.04 Simple disulfide: pdb=" SG CYS A 313 " - pdb=" SG CYS A 316 " distance=2.03 Simple disulfide: pdb=" SG CYS B 4 " - pdb=" SG CYS B 15 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 143 " distance=2.03 Simple disulfide: pdb=" SG CYS B 179 " - pdb=" SG CYS B 223 " distance=2.03 Simple disulfide: pdb=" SG CYS B 280 " - pdb=" SG CYS B 329 " distance=2.03 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 312 " distance=2.04 Simple disulfide: pdb=" SG CYS B 313 " - pdb=" SG CYS B 316 " distance=2.03 Simple disulfide: pdb=" SG CYS a 4 " - pdb=" SG CYS a 15 " distance=2.03 Simple disulfide: pdb=" SG CYS a 55 " - pdb=" SG CYS a 143 " distance=2.03 Simple disulfide: pdb=" SG CYS a 179 " - pdb=" SG CYS a 223 " distance=2.03 Simple disulfide: pdb=" SG CYS a 280 " - pdb=" SG CYS a 329 " distance=2.03 Simple disulfide: pdb=" SG CYS a 291 " - pdb=" SG CYS a 312 " distance=2.03 Simple disulfide: pdb=" SG CYS a 313 " - pdb=" SG CYS a 316 " distance=2.03 Simple disulfide: pdb=" SG CYS b 4 " - pdb=" SG CYS b 15 " distance=2.03 Simple disulfide: pdb=" SG CYS b 55 " - pdb=" SG CYS b 143 " distance=2.03 Simple disulfide: pdb=" SG CYS b 179 " - pdb=" SG CYS b 223 " distance=2.03 Simple disulfide: pdb=" SG CYS b 280 " - pdb=" SG CYS b 329 " distance=2.03 Simple disulfide: pdb=" SG CYS b 291 " - pdb=" SG CYS b 312 " distance=2.03 Simple disulfide: pdb=" SG CYS b 313 " - pdb=" SG CYS b 316 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.75 Conformation dependent library (CDL) restraints added in 2.1 seconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2506 Finding SS restraints... Secondary structure from input PDB file: 31 helices and 18 sheets defined 19.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 38 through 53 removed outlier: 4.086A pdb=" N ALA A 44 " --> pdb=" O ARG A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 82 removed outlier: 4.923A pdb=" N GLY A 73 " --> pdb=" O ARG A 69 " (cutoff:3.500A) removed outlier: 5.709A pdb=" N GLU A 74 " --> pdb=" O SER A 70 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N ASN A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 144 through 146 No H-bonds generated for 'chain 'A' and resid 144 through 146' Processing helix chain 'A' and resid 226 through 230 Processing helix chain 'A' and resid 237 through 241 removed outlier: 3.529A pdb=" N LEU A 241 " --> pdb=" O GLU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 248 Processing helix chain 'A' and resid 252 through 256 removed outlier: 3.681A pdb=" N THR A 256 " --> pdb=" O HIS A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.544A pdb=" N ASN A 344 " --> pdb=" O PRO A 341 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU A 345 " --> pdb=" O GLU A 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 341 through 345' Processing helix chain 'B' and resid 38 through 52 removed outlier: 3.615A pdb=" N ALA B 43 " --> pdb=" O PRO B 39 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ALA B 44 " --> pdb=" O ARG B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 71 Processing helix chain 'B' and resid 71 through 83 removed outlier: 3.661A pdb=" N GLU B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N GLU B 81 " --> pdb=" O ALA B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 226 through 230 Processing helix chain 'B' and resid 237 through 241 Processing helix chain 'B' and resid 244 through 248 Processing helix chain 'B' and resid 252 through 256 Processing helix chain 'B' and resid 341 through 345 removed outlier: 4.066A pdb=" N ASN B 344 " --> pdb=" O PRO B 341 " (cutoff:3.500A) Processing helix chain 'a' and resid 38 through 52 Processing helix chain 'a' and resid 61 through 82 removed outlier: 4.828A pdb=" N GLY a 73 " --> pdb=" O ARG a 69 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N GLU a 74 " --> pdb=" O SER a 70 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA a 77 " --> pdb=" O GLY a 73 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N GLU a 80 " --> pdb=" O ASN a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 144 through 146 No H-bonds generated for 'chain 'a' and resid 144 through 146' Processing helix chain 'a' and resid 226 through 230 Processing helix chain 'a' and resid 237 through 241 Processing helix chain 'a' and resid 244 through 248 Processing helix chain 'a' and resid 252 through 256 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'b' and resid 24 through 28 removed outlier: 3.597A pdb=" N TRP b 28 " --> pdb=" O VAL b 25 " (cutoff:3.500A) Processing helix chain 'b' and resid 38 through 53 Processing helix chain 'b' and resid 61 through 82 removed outlier: 4.368A pdb=" N GLY b 73 " --> pdb=" O ARG b 69 " (cutoff:3.500A) removed outlier: 4.703A pdb=" N GLU b 74 " --> pdb=" O SER b 70 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN b 76 " --> pdb=" O GLU b 72 " (cutoff:3.500A) removed outlier: 5.523A pdb=" N ALA b 77 " --> pdb=" O GLY b 73 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N ILE b 78 " --> pdb=" O GLU b 74 " (cutoff:3.500A) Processing helix chain 'b' and resid 226 through 230 Processing helix chain 'b' and resid 237 through 241 removed outlier: 3.611A pdb=" N LEU b 241 " --> pdb=" O GLU b 238 " (cutoff:3.500A) Processing helix chain 'b' and resid 244 through 248 removed outlier: 3.659A pdb=" N ALA b 248 " --> pdb=" O LYS b 245 " (cutoff:3.500A) Processing helix chain 'b' and resid 252 through 256 removed outlier: 3.501A pdb=" N THR b 256 " --> pdb=" O HIS b 253 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 7 removed outlier: 3.531A pdb=" N ASP A 7 " --> pdb=" O GLU A 12 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N GLU A 12 " --> pdb=" O ASP A 7 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N VAL a 2 " --> pdb=" O VAL A 6 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 36 removed outlier: 6.672A pdb=" N SER A 166 " --> pdb=" O HIS A 158 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N HIS A 158 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N TRP A 168 " --> pdb=" O GLU A 156 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 56 through 57 removed outlier: 7.118A pdb=" N GLY A 56 " --> pdb=" O ALA A 149 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 87 through 90 removed outlier: 6.509A pdb=" N THR A 87 " --> pdb=" O PHE A 133 " (cutoff:3.500A) removed outlier: 7.288A pdb=" N VAL A 135 " --> pdb=" O THR A 87 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 89 " --> pdb=" O VAL A 135 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 329 through 331 removed outlier: 3.616A pdb=" N GLU A 274 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 7.128A pdb=" N GLU A 203 " --> pdb=" O LYS A 213 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N ALA A 215 " --> pdb=" O TRP A 201 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N TRP A 201 " --> pdb=" O ALA A 215 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA A 193 " --> pdb=" O SER A 204 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ALA a 193 " --> pdb=" O SER a 204 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG a 214 " --> pdb=" O GLU a 203 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N GLU a 205 " --> pdb=" O LEU a 212 " (cutoff:3.500A) removed outlier: 5.597A pdb=" N LEU a 212 " --> pdb=" O GLU a 205 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N LYS a 213 " --> pdb=" O PHE a 277 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N PHE a 277 " --> pdb=" O LYS a 213 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N GLU a 274 " --> pdb=" O ARG a 324 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE a 323 " --> pdb=" O TRP a 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 284 through 287 Processing sheet with id=AA7, first strand: chain 'B' and resid 2 through 7 removed outlier: 3.659A pdb=" N GLU B 12 " --> pdb=" O ASP B 7 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N GLU b 12 " --> pdb=" O ASP b 7 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL b 2 " --> pdb=" O VAL B 6 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 34 through 35 removed outlier: 3.658A pdb=" N HIS B 35 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 328 through 331 removed outlier: 3.748A pdb=" N GLU B 274 " --> pdb=" O ARG B 324 " (cutoff:3.500A) removed outlier: 5.820A pdb=" N LEU B 212 " --> pdb=" O GLU B 205 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N GLU B 205 " --> pdb=" O LEU B 212 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG B 214 " --> pdb=" O GLU B 203 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N ALA B 193 " --> pdb=" O SER B 204 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLU b 192 " --> pdb=" O LYS b 189 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER b 204 " --> pdb=" O ALA b 193 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ARG b 214 " --> pdb=" O GLU b 203 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N GLU b 205 " --> pdb=" O LEU b 212 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LEU b 212 " --> pdb=" O GLU b 205 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 311 through 313 Processing sheet with id=AB2, first strand: chain 'a' and resid 33 through 36 removed outlier: 6.109A pdb=" N LYS a 33 " --> pdb=" O VAL a 167 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU a 169 " --> pdb=" O LYS a 33 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N HIS a 35 " --> pdb=" O LEU a 169 " (cutoff:3.500A) removed outlier: 8.475A pdb=" N VAL a 171 " --> pdb=" O HIS a 35 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 56 through 58 Processing sheet with id=AB4, first strand: chain 'a' and resid 88 through 89 Processing sheet with id=AB5, first strand: chain 'a' and resid 284 through 287 Processing sheet with id=AB6, first strand: chain 'b' and resid 87 through 89 Processing sheet with id=AB7, first strand: chain 'b' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'b' and resid 284 through 287 removed outlier: 3.787A pdb=" N TRP b 311 " --> pdb=" O LYS b 284 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N CYS b 313 " --> pdb=" O HIS b 286 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'b' and resid 298 through 299 removed outlier: 3.634A pdb=" N LEU b 298 " --> pdb=" O TYR b 331 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 726 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 4.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 3609 1.35 - 1.47: 2674 1.47 - 1.59: 4750 1.59 - 1.71: 0 1.71 - 1.83: 112 Bond restraints: 11145 Sorted by residual: bond pdb=" N VAL b 162 " pdb=" CA VAL b 162 " ideal model delta sigma weight residual 1.457 1.495 -0.038 1.15e-02 7.56e+03 1.11e+01 bond pdb=" N VAL A 25 " pdb=" CA VAL A 25 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.25e-02 6.40e+03 9.13e+00 bond pdb=" N PHE b 160 " pdb=" CA PHE b 160 " ideal model delta sigma weight residual 1.458 1.488 -0.031 1.30e-02 5.92e+03 5.59e+00 bond pdb=" N ASP A 24 " pdb=" CA ASP A 24 " ideal model delta sigma weight residual 1.460 1.493 -0.033 1.42e-02 4.96e+03 5.42e+00 bond pdb=" N ASN a 207 " pdb=" CA ASN a 207 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.42e+00 ... (remaining 11140 not shown) Histogram of bond angle deviations from ideal: 100.44 - 107.16: 476 107.16 - 113.88: 6209 113.88 - 120.60: 4021 120.60 - 127.33: 4167 127.33 - 134.05: 233 Bond angle restraints: 15106 Sorted by residual: angle pdb=" N ASP A 208 " pdb=" CA ASP A 208 " pdb=" C ASP A 208 " ideal model delta sigma weight residual 112.72 107.72 5.00 1.28e+00 6.10e-01 1.52e+01 angle pdb=" CA TRP A 28 " pdb=" C TRP A 28 " pdb=" N ARG A 29 " ideal model delta sigma weight residual 118.13 123.11 -4.98 1.28e+00 6.10e-01 1.51e+01 angle pdb=" N ILE b 242 " pdb=" CA ILE b 242 " pdb=" C ILE b 242 " ideal model delta sigma weight residual 111.48 107.94 3.54 9.40e-01 1.13e+00 1.42e+01 angle pdb=" CA ASP A 24 " pdb=" C ASP A 24 " pdb=" O ASP A 24 " ideal model delta sigma weight residual 122.27 117.95 4.32 1.16e+00 7.43e-01 1.39e+01 angle pdb=" C ASN a 207 " pdb=" CA ASN a 207 " pdb=" CB ASN a 207 " ideal model delta sigma weight residual 110.42 117.04 -6.62 1.99e+00 2.53e-01 1.11e+01 ... (remaining 15101 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 6135 17.60 - 35.19: 444 35.19 - 52.79: 91 52.79 - 70.39: 24 70.39 - 87.98: 7 Dihedral angle restraints: 6701 sinusoidal: 2816 harmonic: 3885 Sorted by residual: dihedral pdb=" CB CYS b 291 " pdb=" SG CYS b 291 " pdb=" SG CYS b 312 " pdb=" CB CYS b 312 " ideal model delta sinusoidal sigma weight residual -86.00 -173.98 87.98 1 1.00e+01 1.00e-02 9.26e+01 dihedral pdb=" CB CYS b 313 " pdb=" SG CYS b 313 " pdb=" SG CYS b 316 " pdb=" CB CYS b 316 " ideal model delta sinusoidal sigma weight residual -86.00 -151.55 65.55 1 1.00e+01 1.00e-02 5.63e+01 dihedral pdb=" CB CYS a 313 " pdb=" SG CYS a 313 " pdb=" SG CYS a 316 " pdb=" CB CYS a 316 " ideal model delta sinusoidal sigma weight residual 93.00 156.86 -63.86 1 1.00e+01 1.00e-02 5.37e+01 ... (remaining 6698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1235 0.043 - 0.085: 214 0.085 - 0.128: 126 0.128 - 0.170: 7 0.170 - 0.213: 2 Chirality restraints: 1584 Sorted by residual: chirality pdb=" CA VAL A 25 " pdb=" N VAL A 25 " pdb=" C VAL A 25 " pdb=" CB VAL A 25 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA VAL b 162 " pdb=" N VAL b 162 " pdb=" C VAL b 162 " pdb=" CB VAL b 162 " both_signs ideal model delta sigma weight residual False 2.44 2.64 -0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CB VAL A 25 " pdb=" CA VAL A 25 " pdb=" CG1 VAL A 25 " pdb=" CG2 VAL A 25 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.55e-01 ... (remaining 1581 not shown) Planarity restraints: 1945 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 100 " 0.031 5.00e-02 4.00e+02 4.72e-02 3.56e+00 pdb=" N PRO A 101 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 101 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 101 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP a 208 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.78e+00 pdb=" C ASP a 208 " -0.029 2.00e-02 2.50e+03 pdb=" O ASP a 208 " 0.011 2.00e-02 2.50e+03 pdb=" N THR a 209 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN b 95 " 0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO b 96 " -0.064 5.00e-02 4.00e+02 pdb=" CA PRO b 96 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO b 96 " 0.019 5.00e-02 4.00e+02 ... (remaining 1942 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 837 2.74 - 3.28: 10584 3.28 - 3.82: 16278 3.82 - 4.36: 20013 4.36 - 4.90: 36068 Nonbonded interactions: 83780 Sorted by model distance: nonbonded pdb=" OG SER B 322 " pdb=" NH1 ARG B 324 " model vdw 2.197 3.120 nonbonded pdb=" NH1 ARG b 299 " pdb=" O THR b 301 " model vdw 2.206 3.120 nonbonded pdb=" OG SER B 61 " pdb=" OE1 GLU B 219 " model vdw 2.228 3.040 nonbonded pdb=" OE2 GLU a 72 " pdb=" ND2 ASN a 76 " model vdw 2.236 3.120 nonbonded pdb=" OG SER b 322 " pdb=" NH1 ARG b 324 " model vdw 2.243 3.120 ... (remaining 83775 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 107 or resid 130 through 352)) selection = (chain 'B' and (resid 1 through 107 or resid 130 through 352)) selection = chain 'a' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.690 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: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 31.540 Find NCS groups from input model: 0.600 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: 0.010 Load rotamer database and sin/cos tables:2.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11145 Z= 0.184 Angle : 0.582 6.617 15106 Z= 0.343 Chirality : 0.042 0.213 1584 Planarity : 0.004 0.047 1945 Dihedral : 13.023 87.838 4123 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.99 % Favored : 94.86 % Rotamer: Outliers : 0.17 % Allowed : 0.17 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.24), residues: 1343 helix: 1.10 (0.44), residues: 148 sheet: -1.73 (0.36), residues: 225 loop : -0.78 (0.21), residues: 970 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP a 232 HIS 0.004 0.001 HIS b 254 PHE 0.011 0.001 PHE A 123 TYR 0.010 0.001 TYR B 32 ARG 0.002 0.000 ARG a 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 204 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7669 (tpp80) REVERT: A 156 GLU cc_start: 0.7451 (pt0) cc_final: 0.7196 (pt0) REVERT: A 274 GLU cc_start: 0.8077 (tt0) cc_final: 0.7687 (mt-10) REVERT: a 207 ASN cc_start: 0.7381 (t0) cc_final: 0.6814 (t0) REVERT: a 208 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.6865 (t0) REVERT: a 251 LEU cc_start: 0.8657 (mp) cc_final: 0.8389 (mp) REVERT: a 315 GLU cc_start: 0.8065 (tt0) cc_final: 0.7557 (tp30) REVERT: b 67 MET cc_start: 0.6248 (tmm) cc_final: 0.6040 (tmm) REVERT: b 330 TRP cc_start: 0.6650 (m100) cc_final: 0.6196 (m-10) outliers start: 2 outliers final: 0 residues processed: 204 average time/residue: 0.2741 time to fit residues: 75.1349 Evaluate side-chains 121 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 120 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 208 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 102 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 69 optimal weight: 0.4980 chunk 54 optimal weight: 0.8980 chunk 105 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 64 optimal weight: 10.0000 chunk 78 optimal weight: 3.9990 chunk 122 optimal weight: 0.0670 overall best weight: 2.0922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 48 GLN A 207 ASN B 35 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 82 ASN a 76 ASN a 207 ASN b 35 HIS b 269 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.1674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 11145 Z= 0.309 Angle : 0.640 7.773 15106 Z= 0.339 Chirality : 0.046 0.178 1584 Planarity : 0.005 0.047 1945 Dihedral : 5.274 51.237 1478 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 1.51 % Allowed : 7.40 % Favored : 91.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1343 helix: 1.00 (0.42), residues: 159 sheet: -1.73 (0.32), residues: 279 loop : -0.80 (0.21), residues: 905 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP a 232 HIS 0.006 0.001 HIS b 254 PHE 0.029 0.002 PHE B 277 TYR 0.017 0.002 TYR a 331 ARG 0.005 0.001 ARG B 314 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 137 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 ASP cc_start: 0.6386 (t0) cc_final: 0.6165 (t0) REVERT: A 97 MET cc_start: 0.8610 (mtm) cc_final: 0.8343 (mtt) REVERT: A 274 GLU cc_start: 0.7941 (tt0) cc_final: 0.7363 (mt-10) REVERT: A 333 MET cc_start: 0.6200 (OUTLIER) cc_final: 0.5735 (mtp) REVERT: B 339 LYS cc_start: 0.7286 (pttm) cc_final: 0.6843 (ptmm) REVERT: a 69 ARG cc_start: 0.7182 (ptp-170) cc_final: 0.6854 (tpp80) REVERT: a 146 LYS cc_start: 0.8084 (mtpt) cc_final: 0.7834 (mmtt) REVERT: b 67 MET cc_start: 0.6298 (tmm) cc_final: 0.6000 (tmm) outliers start: 18 outliers final: 14 residues processed: 147 average time/residue: 0.2518 time to fit residues: 51.6605 Evaluate side-chains 130 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 115 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 5 SER Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 8.9990 chunk 38 optimal weight: 0.7980 chunk 102 optimal weight: 5.9990 chunk 83 optimal weight: 8.9990 chunk 33 optimal weight: 1.9990 chunk 122 optimal weight: 0.9990 chunk 132 optimal weight: 0.0770 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 overall best weight: 0.7142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 344 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11145 Z= 0.181 Angle : 0.563 11.215 15106 Z= 0.295 Chirality : 0.042 0.219 1584 Planarity : 0.004 0.036 1945 Dihedral : 4.579 19.362 1476 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 3.75 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.87 % Favored : 96.05 % Rotamer: Outliers : 1.60 % Allowed : 9.25 % Favored : 89.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.24), residues: 1343 helix: 1.22 (0.42), residues: 159 sheet: -1.76 (0.32), residues: 277 loop : -0.74 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP a 330 HIS 0.004 0.001 HIS b 254 PHE 0.020 0.001 PHE B 277 TYR 0.012 0.001 TYR A 331 ARG 0.005 0.000 ARG a 324 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 138 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 GLU cc_start: 0.7863 (tt0) cc_final: 0.7285 (mt-10) REVERT: A 333 MET cc_start: 0.6241 (OUTLIER) cc_final: 0.5849 (mtp) REVERT: B 263 GLN cc_start: 0.7319 (mp10) cc_final: 0.7016 (mt0) REVERT: B 339 LYS cc_start: 0.7188 (pttm) cc_final: 0.6854 (ptmm) REVERT: a 146 LYS cc_start: 0.8114 (mtpt) cc_final: 0.7862 (mmtt) REVERT: a 324 ARG cc_start: 0.8326 (mmt-90) cc_final: 0.8087 (mmt-90) REVERT: b 67 MET cc_start: 0.6265 (tmm) cc_final: 0.5975 (tmm) outliers start: 19 outliers final: 11 residues processed: 149 average time/residue: 0.2566 time to fit residues: 52.7185 Evaluate side-chains 134 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 122 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 333 MET Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 121 optimal weight: 6.9990 chunk 92 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 13 optimal weight: 0.0670 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 116 optimal weight: 0.0870 chunk 35 optimal weight: 8.9990 overall best weight: 1.8300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN B 254 HIS ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11145 Z= 0.277 Angle : 0.611 14.258 15106 Z= 0.318 Chirality : 0.044 0.233 1584 Planarity : 0.004 0.042 1945 Dihedral : 4.713 19.004 1476 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.81 % Favored : 94.12 % Rotamer: Outliers : 3.11 % Allowed : 10.18 % Favored : 86.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.26 (0.23), residues: 1343 helix: 1.17 (0.42), residues: 159 sheet: -1.83 (0.32), residues: 281 loop : -0.87 (0.21), residues: 903 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.006 0.001 HIS b 254 PHE 0.019 0.002 PHE B 277 TYR 0.012 0.001 TYR B 34 ARG 0.005 0.000 ARG A 40 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 134 time to evaluate : 1.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 97 MET cc_start: 0.8538 (mtm) cc_final: 0.8228 (mtt) REVERT: B 263 GLN cc_start: 0.7446 (mp10) cc_final: 0.7067 (mt0) REVERT: B 339 LYS cc_start: 0.7317 (pttm) cc_final: 0.7015 (ptmm) REVERT: a 146 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7996 (mmtt) REVERT: a 333 MET cc_start: 0.8182 (mmp) cc_final: 0.6957 (mmm) REVERT: b 67 MET cc_start: 0.6433 (tmm) cc_final: 0.6104 (tmm) outliers start: 37 outliers final: 26 residues processed: 157 average time/residue: 0.2326 time to fit residues: 51.5718 Evaluate side-chains 145 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 108 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 1 optimal weight: 8.9990 chunk 97 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 111 optimal weight: 0.8980 chunk 90 optimal weight: 5.9990 chunk 0 optimal weight: 3.9990 chunk 66 optimal weight: 7.9990 chunk 117 optimal weight: 0.6980 chunk 32 optimal weight: 0.3980 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7519 moved from start: 0.2543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11145 Z= 0.290 Angle : 0.616 13.268 15106 Z= 0.321 Chirality : 0.045 0.226 1584 Planarity : 0.004 0.040 1945 Dihedral : 4.744 18.221 1476 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.66 % Favored : 94.19 % Rotamer: Outliers : 3.11 % Allowed : 11.52 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.23), residues: 1343 helix: 1.02 (0.42), residues: 159 sheet: -1.65 (0.33), residues: 277 loop : -1.06 (0.21), residues: 907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.006 0.001 HIS B 254 PHE 0.017 0.002 PHE B 277 TYR 0.011 0.001 TYR B 34 ARG 0.008 0.000 ARG b 261 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 138 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 ASP cc_start: 0.8357 (t0) cc_final: 0.8116 (t0) REVERT: A 40 ARG cc_start: 0.8361 (tpp80) cc_final: 0.7937 (tpp80) REVERT: A 97 MET cc_start: 0.8556 (mtm) cc_final: 0.8243 (mtt) REVERT: B 339 LYS cc_start: 0.7457 (pttm) cc_final: 0.7248 (ptmm) REVERT: a 146 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7982 (mmtm) REVERT: a 311 TRP cc_start: 0.6523 (m100) cc_final: 0.6158 (m100) REVERT: a 333 MET cc_start: 0.8240 (mmp) cc_final: 0.7346 (mmm) outliers start: 37 outliers final: 31 residues processed: 162 average time/residue: 0.2489 time to fit residues: 56.8291 Evaluate side-chains 152 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 121 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 7.9990 chunk 117 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 76 optimal weight: 10.0000 chunk 32 optimal weight: 8.9990 chunk 130 optimal weight: 9.9990 chunk 108 optimal weight: 9.9990 chunk 60 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 125 optimal weight: 6.9990 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN ** b 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 11145 Z= 0.328 Angle : 0.649 12.505 15106 Z= 0.337 Chirality : 0.046 0.225 1584 Planarity : 0.004 0.042 1945 Dihedral : 4.866 22.540 1476 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.22 % Favored : 92.63 % Rotamer: Outliers : 3.53 % Allowed : 13.04 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.23), residues: 1343 helix: 0.88 (0.41), residues: 160 sheet: -1.73 (0.33), residues: 277 loop : -1.17 (0.21), residues: 906 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.007 0.001 HIS B 254 PHE 0.017 0.002 PHE B 277 TYR 0.012 0.002 TYR A 331 ARG 0.008 0.001 ARG b 261 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 126 time to evaluate : 1.318 Fit side-chains revert: symmetry clash REVERT: A 97 MET cc_start: 0.8583 (mtm) cc_final: 0.8272 (mtt) REVERT: A 331 TYR cc_start: 0.6893 (OUTLIER) cc_final: 0.5245 (t80) REVERT: B 264 MET cc_start: 0.7612 (mmt) cc_final: 0.7356 (mmm) REVERT: a 69 ARG cc_start: 0.7277 (ptp-170) cc_final: 0.6879 (tpp80) REVERT: a 146 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7943 (mmtm) REVERT: a 311 TRP cc_start: 0.6698 (m100) cc_final: 0.6329 (m100) REVERT: b 67 MET cc_start: 0.6428 (tmm) cc_final: 0.6109 (tmm) REVERT: b 265 LYS cc_start: 0.7164 (mtpt) cc_final: 0.6758 (mtpt) outliers start: 42 outliers final: 33 residues processed: 154 average time/residue: 0.2322 time to fit residues: 51.0274 Evaluate side-chains 146 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 112 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 154 LEU Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 218 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 12 GLU Chi-restraints excluded: chain B residue 57 ILE Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 231 LEU Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 9 SER Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Chi-restraints excluded: chain b residue 252 SER Chi-restraints excluded: chain b residue 283 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 95 optimal weight: 0.0970 chunk 73 optimal weight: 5.9990 chunk 109 optimal weight: 9.9990 chunk 72 optimal weight: 0.9980 chunk 130 optimal weight: 0.5980 chunk 81 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 overall best weight: 0.6978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11145 Z= 0.175 Angle : 0.565 11.859 15106 Z= 0.292 Chirality : 0.042 0.193 1584 Planarity : 0.004 0.041 1945 Dihedral : 4.353 17.532 1476 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.39 % Favored : 95.46 % Rotamer: Outliers : 2.27 % Allowed : 14.63 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.23), residues: 1343 helix: 0.96 (0.41), residues: 160 sheet: -1.57 (0.34), residues: 261 loop : -0.98 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP a 330 HIS 0.003 0.001 HIS b 147 PHE 0.016 0.001 PHE B 277 TYR 0.007 0.001 TYR b 260 ARG 0.006 0.000 ARG b 261 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 129 time to evaluate : 1.207 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 141 LYS cc_start: 0.7489 (pptt) cc_final: 0.6808 (ttpp) REVERT: B 264 MET cc_start: 0.7481 (mmt) cc_final: 0.7278 (mmm) REVERT: a 33 LYS cc_start: 0.7040 (tppt) cc_final: 0.6262 (tmtt) REVERT: a 146 LYS cc_start: 0.8133 (mtpt) cc_final: 0.7918 (mmtm) REVERT: a 333 MET cc_start: 0.7862 (mmp) cc_final: 0.6804 (mmm) REVERT: b 67 MET cc_start: 0.6395 (tmm) cc_final: 0.6087 (tmm) REVERT: b 265 LYS cc_start: 0.6880 (mtpt) cc_final: 0.6575 (mtpt) outliers start: 27 outliers final: 21 residues processed: 148 average time/residue: 0.2294 time to fit residues: 48.2287 Evaluate side-chains 141 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 120 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 71 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 chunk 82 optimal weight: 6.9990 chunk 88 optimal weight: 0.9990 chunk 64 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 102 optimal weight: 0.8980 chunk 118 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 207 ASN B 95 ASN b 95 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 11145 Z= 0.228 Angle : 0.589 11.104 15106 Z= 0.303 Chirality : 0.044 0.196 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.422 17.768 1476 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 2.69 % Allowed : 15.22 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.23), residues: 1343 helix: 0.94 (0.41), residues: 160 sheet: -1.59 (0.34), residues: 261 loop : -1.02 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 311 HIS 0.005 0.001 HIS b 254 PHE 0.015 0.002 PHE B 277 TYR 0.010 0.001 TYR A 331 ARG 0.004 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 119 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.7199 (m-10) cc_final: 0.6868 (m-10) REVERT: A 331 TYR cc_start: 0.6798 (OUTLIER) cc_final: 0.5358 (t80) REVERT: B 141 LYS cc_start: 0.7532 (pptt) cc_final: 0.6856 (ttpp) REVERT: a 33 LYS cc_start: 0.7099 (tppt) cc_final: 0.6294 (tmtt) REVERT: a 69 ARG cc_start: 0.7241 (ptp-170) cc_final: 0.6821 (tpp80) REVERT: a 146 LYS cc_start: 0.8169 (mtpt) cc_final: 0.7952 (mmtt) REVERT: a 333 MET cc_start: 0.7948 (mmp) cc_final: 0.7002 (mmm) REVERT: b 67 MET cc_start: 0.6404 (tmm) cc_final: 0.5970 (tmm) outliers start: 32 outliers final: 26 residues processed: 140 average time/residue: 0.2257 time to fit residues: 45.9667 Evaluate side-chains 139 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 112 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 154 LEU Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 8.9990 chunk 121 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 72 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 120 optimal weight: 0.0980 chunk 79 optimal weight: 4.9990 overall best weight: 1.8188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11145 Z= 0.274 Angle : 0.615 13.900 15106 Z= 0.318 Chirality : 0.044 0.196 1584 Planarity : 0.004 0.038 1945 Dihedral : 4.551 18.676 1476 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.15 % Allowed : 6.03 % Favored : 93.82 % Rotamer: Outliers : 2.69 % Allowed : 15.22 % Favored : 82.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.23), residues: 1343 helix: 0.89 (0.40), residues: 160 sheet: -1.64 (0.34), residues: 261 loop : -1.09 (0.21), residues: 922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP a 311 HIS 0.006 0.001 HIS B 254 PHE 0.015 0.002 PHE B 277 TYR 0.011 0.001 TYR A 331 ARG 0.005 0.000 ARG B 29 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 117 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.7307 (m-10) cc_final: 0.7056 (m-10) REVERT: A 97 MET cc_start: 0.8575 (mtm) cc_final: 0.8263 (mtt) REVERT: A 331 TYR cc_start: 0.6880 (OUTLIER) cc_final: 0.5429 (t80) REVERT: B 141 LYS cc_start: 0.7477 (pptt) cc_final: 0.6797 (ttpp) REVERT: B 198 LEU cc_start: 0.7932 (mt) cc_final: 0.7724 (mt) REVERT: a 33 LYS cc_start: 0.7113 (tppt) cc_final: 0.6292 (tmtt) REVERT: a 69 ARG cc_start: 0.7273 (ptp-170) cc_final: 0.6860 (tpp80) REVERT: a 146 LYS cc_start: 0.8204 (mtpt) cc_final: 0.7971 (mmtm) REVERT: a 333 MET cc_start: 0.7994 (mmp) cc_final: 0.7100 (mmm) outliers start: 32 outliers final: 28 residues processed: 137 average time/residue: 0.2050 time to fit residues: 41.5208 Evaluate side-chains 142 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 113 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 13 THR Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 10.0000 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 3.9990 chunk 89 optimal weight: 0.9980 chunk 134 optimal weight: 7.9990 chunk 123 optimal weight: 4.9990 chunk 107 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 82 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7501 moved from start: 0.3065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 11145 Z= 0.248 Angle : 0.608 13.511 15106 Z= 0.313 Chirality : 0.044 0.185 1584 Planarity : 0.004 0.037 1945 Dihedral : 4.522 18.128 1476 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.15 % Allowed : 5.81 % Favored : 94.04 % Rotamer: Outliers : 2.78 % Allowed : 15.39 % Favored : 81.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.23), residues: 1343 helix: 0.89 (0.40), residues: 160 sheet: -1.56 (0.34), residues: 255 loop : -1.12 (0.21), residues: 928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 311 HIS 0.005 0.001 HIS b 254 PHE 0.015 0.002 PHE B 277 TYR 0.010 0.001 TYR A 331 ARG 0.005 0.000 ARG B 29 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 116 time to evaluate : 1.268 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 TRP cc_start: 0.7281 (m-10) cc_final: 0.7020 (m-10) REVERT: A 331 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.5463 (t80) REVERT: B 141 LYS cc_start: 0.7463 (pptt) cc_final: 0.6796 (ttpp) REVERT: a 33 LYS cc_start: 0.7105 (tppt) cc_final: 0.6297 (tmtt) REVERT: a 69 ARG cc_start: 0.7262 (ptp-170) cc_final: 0.6856 (tpp80) REVERT: a 146 LYS cc_start: 0.8188 (mtpt) cc_final: 0.7953 (mmtm) REVERT: a 333 MET cc_start: 0.8028 (mmp) cc_final: 0.7180 (mmm) outliers start: 33 outliers final: 30 residues processed: 138 average time/residue: 0.2155 time to fit residues: 43.7368 Evaluate side-chains 143 residues out of total 1189 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 112 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 6 VAL Chi-restraints excluded: chain A residue 59 SER Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 139 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 194 VAL Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 231 LEU Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain A residue 331 TYR Chi-restraints excluded: chain B residue 4 CYS Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 67 MET Chi-restraints excluded: chain B residue 95 ASN Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 280 CYS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain a residue 93 VAL Chi-restraints excluded: chain a residue 106 VAL Chi-restraints excluded: chain a residue 157 ASP Chi-restraints excluded: chain a residue 208 ASP Chi-restraints excluded: chain a residue 287 VAL Chi-restraints excluded: chain a residue 302 THR Chi-restraints excluded: chain a residue 350 VAL Chi-restraints excluded: chain b residue 7 ASP Chi-restraints excluded: chain b residue 15 CYS Chi-restraints excluded: chain b residue 17 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 209 THR Chi-restraints excluded: chain b residue 240 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 0.0060 chunk 32 optimal weight: 4.9990 chunk 98 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 107 optimal weight: 30.0000 chunk 44 optimal weight: 2.9990 chunk 110 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 94 optimal weight: 0.9990 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 254 HIS B 95 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.204379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.163108 restraints weight = 12246.454| |-----------------------------------------------------------------------------| r_work (start): 0.3927 rms_B_bonded: 3.37 r_work: 0.3657 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.3097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 11145 Z= 0.360 Angle : 0.678 14.010 15106 Z= 0.351 Chirality : 0.047 0.202 1584 Planarity : 0.004 0.041 1945 Dihedral : 4.803 20.625 1476 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.15 % Allowed : 7.82 % Favored : 92.03 % Rotamer: Outliers : 2.86 % Allowed : 15.64 % Favored : 81.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.81 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.61 (0.23), residues: 1343 helix: 0.72 (0.40), residues: 160 sheet: -1.67 (0.33), residues: 275 loop : -1.24 (0.21), residues: 908 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 311 HIS 0.008 0.001 HIS B 254 PHE 0.016 0.002 PHE A 133 TYR 0.014 0.002 TYR A 331 ARG 0.005 0.000 ARG B 29 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2520.61 seconds wall clock time: 45 minutes 55.64 seconds (2755.64 seconds total)