Starting phenix.real_space_refine on Sun Jul 27 06:19:53 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.map" model { file = "/net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zpa_14852/07_2025/7zpa_14852.cif" } resolution = 3.9 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= 0.008 sd= 0.925 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: 5 Type Number sf(0) Gaussians P 97 5.49 5 S 18 5.16 5 C 5544 2.51 5 N 1574 2.21 5 O 1888 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 9121 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3538 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 431, 3530 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 412} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 3605 Chain: "B" Number of atoms: 3636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 443, 3636 Classifications: {'peptide': 443} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 422} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'LLP:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 975 Classifications: {'DNA': 48} Link IDs: {'rna3p': 47} Chain: "D" Number of atoms: 972 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 972 Classifications: {'DNA': 47} Link IDs: {'rna3p': 46} Time building chain proxies: 7.64, per 1000 atoms: 0.84 Number of scatterers: 9121 At special positions: 0 Unit cell: (83.566, 101.346, 136.906, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 P 97 15.00 O 1888 8.00 N 1574 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 2.15 Conformation dependent library (CDL) restraints added in 1.1 seconds 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1654 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 8 sheets defined 46.5% alpha, 9.0% beta 12 base pairs and 50 stacking pairs defined. Time for finding SS restraints: 3.19 Creating SS restraints... Processing helix chain 'A' and resid 15 through 31 removed outlier: 4.480A pdb=" N TYR A 21 " --> pdb=" O TYR A 17 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU A 27 " --> pdb=" O HIS A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 50 Processing helix chain 'A' and resid 52 through 66 removed outlier: 3.592A pdb=" N VAL A 56 " --> pdb=" O SER A 52 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLU A 66 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.779A pdb=" N LYS A 126 " --> pdb=" O GLU A 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N TYR A 127 " --> pdb=" O GLN A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 164 removed outlier: 3.545A pdb=" N GLY A 164 " --> pdb=" O HIS A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 190 removed outlier: 4.366A pdb=" N THR A 180 " --> pdb=" O ALA A 176 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LEU A 181 " --> pdb=" O GLY A 177 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 212 removed outlier: 4.344A pdb=" N HIS A 211 " --> pdb=" O LYS A 207 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 212 " --> pdb=" O LEU A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 233 Processing helix chain 'A' and resid 254 through 267 removed outlier: 3.727A pdb=" N ARG A 258 " --> pdb=" O SER A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 295 Processing helix chain 'A' and resid 323 through 334 Processing helix chain 'A' and resid 342 through 356 removed outlier: 3.936A pdb=" N GLN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 381 removed outlier: 4.065A pdb=" N LYS A 360 " --> pdb=" O GLY A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 407 through 418 Processing helix chain 'A' and resid 426 through 428 No H-bonds generated for 'chain 'A' and resid 426 through 428' Processing helix chain 'A' and resid 450 through 462 Processing helix chain 'B' and resid 15 through 31 removed outlier: 4.711A pdb=" N TYR B 21 " --> pdb=" O TYR B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 49 Processing helix chain 'B' and resid 52 through 67 removed outlier: 3.601A pdb=" N VAL B 56 " --> pdb=" O SER B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 120 through 132 removed outlier: 3.876A pdb=" N LYS B 126 " --> pdb=" O GLU B 122 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N TYR B 127 " --> pdb=" O GLN B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 164 Processing helix chain 'B' and resid 168 through 172 Processing helix chain 'B' and resid 176 through 190 removed outlier: 4.357A pdb=" N THR B 180 " --> pdb=" O ALA B 176 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LEU B 181 " --> pdb=" O GLY B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 210 Processing helix chain 'B' and resid 227 through 233 Processing helix chain 'B' and resid 254 through 268 removed outlier: 3.872A pdb=" N HIS B 268 " --> pdb=" O TRP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 296 Processing helix chain 'B' and resid 323 through 334 Processing helix chain 'B' and resid 342 through 355 removed outlier: 3.709A pdb=" N GLN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 381 removed outlier: 3.804A pdb=" N LYS B 360 " --> pdb=" O GLY B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 407 through 418 Processing helix chain 'B' and resid 447 through 449 No H-bonds generated for 'chain 'B' and resid 447 through 449' Processing helix chain 'B' and resid 450 through 462 Processing sheet with id=AA1, first strand: chain 'A' and resid 69 through 72 removed outlier: 3.991A pdb=" N GLY A 76 " --> pdb=" O ILE A 72 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 108 removed outlier: 6.618A pdb=" N TYR A 107 " --> pdb=" O LYS A 421 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 172 through 175 removed outlier: 3.609A pdb=" N GLY A 175 " --> pdb=" O SER A 318 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ILE A 273 " --> pdb=" O ILE A 302 " (cutoff:3.500A) removed outlier: 7.401A pdb=" N LEU A 304 " --> pdb=" O ILE A 273 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLU A 275 " --> pdb=" O LEU A 304 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL A 239 " --> pdb=" O ILE A 274 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N ASP A 276 " --> pdb=" O VAL A 239 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N THR A 241 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N VAL A 194 " --> pdb=" O VAL A 238 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N TYR A 240 " --> pdb=" O VAL A 194 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY A 196 " --> pdb=" O TYR A 240 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 195 " --> pdb=" O VAL A 217 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N PHE A 219 " --> pdb=" O TYR A 195 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE A 197 " --> pdb=" O PHE A 219 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 387 through 390 removed outlier: 3.815A pdb=" N LEU A 388 " --> pdb=" O VAL A 401 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL A 401 " --> pdb=" O LEU A 388 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N VAL A 399 " --> pdb=" O ILE A 390 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL A 440 " --> pdb=" O TYR A 423 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N TYR A 423 " --> pdb=" O VAL A 440 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 69 through 71 Processing sheet with id=AA6, first strand: chain 'B' and resid 173 through 175 removed outlier: 3.592A pdb=" N GLY B 175 " --> pdb=" O SER B 318 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 215 through 217 removed outlier: 6.285A pdb=" N VAL B 194 " --> pdb=" O VAL B 238 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N TYR B 240 " --> pdb=" O VAL B 194 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N GLY B 196 " --> pdb=" O TYR B 240 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL B 239 " --> pdb=" O ILE B 274 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N ASP B 276 " --> pdb=" O VAL B 239 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N THR B 241 " --> pdb=" O ASP B 276 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 387 through 389 removed outlier: 3.643A pdb=" N LEU B 388 " --> pdb=" O VAL B 401 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL B 401 " --> pdb=" O LEU B 388 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL B 440 " --> pdb=" O TYR B 423 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N TYR B 423 " --> pdb=" O VAL B 440 " (cutoff:3.500A) 282 hydrogen bonds defined for protein. 816 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 27 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 12 basepair parallelities 50 stacking parallelities Total time for adding SS restraints: 2.75 Time building geometry restraints manager: 2.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2305 1.33 - 1.45: 2293 1.45 - 1.57: 4711 1.57 - 1.69: 190 1.69 - 1.81: 32 Bond restraints: 9531 Sorted by residual: bond pdb=" OP4 LLP A 309 " pdb=" P LLP A 309 " ideal model delta sigma weight residual 1.726 1.542 0.184 2.00e-02 2.50e+03 8.46e+01 bond pdb=" OP4 LLP B 309 " pdb=" P LLP B 309 " ideal model delta sigma weight residual 1.726 1.546 0.180 2.00e-02 2.50e+03 8.14e+01 bond pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.31e+01 bond pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " ideal model delta sigma weight residual 1.273 1.432 -0.159 2.00e-02 2.50e+03 6.29e+01 bond pdb=" C4 LLP A 309 " pdb=" C4' LLP A 309 " ideal model delta sigma weight residual 1.464 1.614 -0.150 2.00e-02 2.50e+03 5.61e+01 ... (remaining 9526 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 13138 2.47 - 4.94: 155 4.94 - 7.40: 17 7.40 - 9.87: 3 9.87 - 12.34: 3 Bond angle restraints: 13316 Sorted by residual: angle pdb=" N VAL B 297 " pdb=" CA VAL B 297 " pdb=" C VAL B 297 " ideal model delta sigma weight residual 113.53 107.41 6.12 9.80e-01 1.04e+00 3.89e+01 angle pdb=" NZ LLP B 309 " pdb=" C4' LLP B 309 " pdb=" C4 LLP B 309 " ideal model delta sigma weight residual 120.09 107.75 12.34 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C GLU B 66 " pdb=" N GLY B 67 " pdb=" CA GLY B 67 " ideal model delta sigma weight residual 122.69 116.68 6.01 1.59e+00 3.96e-01 1.43e+01 angle pdb=" NZ LLP A 309 " pdb=" C4' LLP A 309 " pdb=" C4 LLP A 309 " ideal model delta sigma weight residual 120.09 109.00 11.09 3.00e+00 1.11e-01 1.37e+01 angle pdb=" CA ARG B 316 " pdb=" C ARG B 316 " pdb=" O ARG B 316 " ideal model delta sigma weight residual 122.44 117.71 4.73 1.32e+00 5.74e-01 1.28e+01 ... (remaining 13311 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 4922 27.53 - 55.07: 486 55.07 - 82.60: 55 82.60 - 110.14: 5 110.14 - 137.67: 1 Dihedral angle restraints: 5469 sinusoidal: 2885 harmonic: 2584 Sorted by residual: dihedral pdb=" CA ARG A 74 " pdb=" C ARG A 74 " pdb=" N LYS A 75 " pdb=" CA LYS A 75 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" CA GLU B 83 " pdb=" C GLU B 83 " pdb=" N ASP B 84 " pdb=" CA ASP B 84 " ideal model delta harmonic sigma weight residual 180.00 160.81 19.19 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" C4' DA D 33 " pdb=" C3' DA D 33 " pdb=" O3' DA D 33 " pdb=" P DA D 34 " ideal model delta sinusoidal sigma weight residual 220.00 82.33 137.67 1 3.50e+01 8.16e-04 1.36e+01 ... (remaining 5466 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 980 0.032 - 0.064: 321 0.064 - 0.097: 103 0.097 - 0.129: 49 0.129 - 0.161: 8 Chirality restraints: 1461 Sorted by residual: chirality pdb=" CB ILE B 273 " pdb=" CA ILE B 273 " pdb=" CG1 ILE B 273 " pdb=" CG2 ILE B 273 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.49e-01 chirality pdb=" CA GLU B 154 " pdb=" N GLU B 154 " pdb=" C GLU B 154 " pdb=" CB GLU B 154 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.24e-01 chirality pdb=" CB VAL A 315 " pdb=" CA VAL A 315 " pdb=" CG1 VAL A 315 " pdb=" CG2 VAL A 315 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1458 not shown) Planarity restraints: 1363 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP A 309 " 0.159 2.00e-02 2.50e+03 2.67e-01 7.10e+02 pdb=" NZ LLP A 309 " -0.359 2.00e-02 2.50e+03 pdb=" C4 LLP A 309 " -0.135 2.00e-02 2.50e+03 pdb=" C4' LLP A 309 " 0.335 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP B 309 " 0.078 2.00e-02 2.50e+03 7.41e-02 5.49e+01 pdb=" NZ LLP B 309 " -0.082 2.00e-02 2.50e+03 pdb=" C4 LLP B 309 " 0.070 2.00e-02 2.50e+03 pdb=" C4' LLP B 309 " -0.066 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 247 " 0.031 5.00e-02 4.00e+02 4.66e-02 3.48e+00 pdb=" N PRO A 248 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 248 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 248 " 0.024 5.00e-02 4.00e+02 ... (remaining 1360 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 1177 2.75 - 3.29: 8854 3.29 - 3.83: 15249 3.83 - 4.36: 16908 4.36 - 4.90: 27536 Nonbonded interactions: 69724 Sorted by model distance: nonbonded pdb=" OG1 THR B 168 " pdb=" OE1 GLN B 171 " model vdw 2.214 3.040 nonbonded pdb=" OG SER A 308 " pdb=" O ILE A 312 " model vdw 2.221 3.040 nonbonded pdb=" OE1 GLN B 184 " pdb=" OH TYR B 330 " model vdw 2.241 3.040 nonbonded pdb=" OH TYR B 240 " pdb=" OD2 ASP B 276 " model vdw 2.244 3.040 nonbonded pdb=" OG SER B 162 " pdb=" OE2 GLU B 281 " model vdw 2.284 3.040 ... (remaining 69719 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 15 through 81 or resid 103 through 442 or resid 444 throug \ h 464)) selection = (chain 'B' and (resid 15 through 81 or resid 84 or resid 104 through 442 or resi \ d 444 through 464)) } 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=0.50 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: 1.210 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: 0.000 Extract box with map and model: 0.410 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.610 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 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 : 0.006 0.184 9531 Z= 0.290 Angle : 0.698 12.341 13316 Z= 0.377 Chirality : 0.040 0.161 1461 Planarity : 0.009 0.267 1363 Dihedral : 19.492 137.671 3815 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.40 (0.29), residues: 861 helix: 0.90 (0.28), residues: 370 sheet: -0.29 (0.50), residues: 107 loop : -1.43 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 23 PHE 0.020 0.002 PHE A 128 TYR 0.018 0.002 TYR A 337 ARG 0.005 0.000 ARG B 316 Details of bonding type rmsd hydrogen bonds : bond 0.16407 ( 309) hydrogen bonds : angle 7.02334 ( 866) covalent geometry : bond 0.00588 ( 9531) covalent geometry : angle 0.69764 (13316) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 32 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7443 (ttm-80) REVERT: A 291 SER cc_start: 0.7372 (m) cc_final: 0.7086 (m) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.2045 time to fit residues: 25.8670 Evaluate side-chains 66 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 9.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 74 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 55 optimal weight: 0.9980 chunk 86 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN B 355 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.120217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.095071 restraints weight = 21130.856| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.097161 restraints weight = 12369.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098596 restraints weight = 8368.461| |-----------------------------------------------------------------------------| r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3517 r_free = 0.3517 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7405 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9531 Z= 0.151 Angle : 0.624 7.808 13316 Z= 0.346 Chirality : 0.041 0.154 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.370 138.428 2059 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.29 % Allowed : 8.13 % Favored : 90.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.37 (0.29), residues: 861 helix: 0.97 (0.27), residues: 376 sheet: -0.53 (0.48), residues: 112 loop : -1.42 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 264 HIS 0.003 0.001 HIS A 160 PHE 0.014 0.002 PHE A 77 TYR 0.022 0.001 TYR B 21 ARG 0.004 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.05676 ( 309) hydrogen bonds : angle 4.45243 ( 866) covalent geometry : bond 0.00332 ( 9531) covalent geometry : angle 0.62409 (13316) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.910 Fit side-chains REVERT: A 32 ARG cc_start: 0.7623 (ttm170) cc_final: 0.7407 (ttm-80) REVERT: A 291 SER cc_start: 0.7089 (m) cc_final: 0.6806 (m) REVERT: A 413 GLU cc_start: 0.8277 (tm-30) cc_final: 0.7810 (tp30) outliers start: 10 outliers final: 6 residues processed: 80 average time/residue: 0.2083 time to fit residues: 23.8546 Evaluate side-chains 73 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 67 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 416 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 82 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 75 optimal weight: 0.6980 chunk 80 optimal weight: 3.9990 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 60 optimal weight: 0.8980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.120604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.095092 restraints weight = 21407.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.097181 restraints weight = 12637.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.098641 restraints weight = 8576.515| |-----------------------------------------------------------------------------| r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3515 r_free = 0.3515 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 moved from start: 0.1721 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9531 Z= 0.146 Angle : 0.596 7.679 13316 Z= 0.333 Chirality : 0.041 0.155 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.490 140.427 2059 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.29 % Allowed : 11.23 % Favored : 87.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.25 (0.29), residues: 861 helix: 1.13 (0.27), residues: 376 sheet: -0.57 (0.47), residues: 112 loop : -1.38 (0.31), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 124 HIS 0.008 0.001 HIS A 145 PHE 0.012 0.002 PHE A 128 TYR 0.018 0.001 TYR B 21 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04947 ( 309) hydrogen bonds : angle 4.12080 ( 866) covalent geometry : bond 0.00320 ( 9531) covalent geometry : angle 0.59606 (13316) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 1.187 Fit side-chains REVERT: A 365 MET cc_start: 0.6093 (mmm) cc_final: 0.5777 (mmm) REVERT: B 115 ASP cc_start: 0.6304 (m-30) cc_final: 0.5841 (m-30) outliers start: 10 outliers final: 6 residues processed: 78 average time/residue: 0.2337 time to fit residues: 27.6844 Evaluate side-chains 72 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 66 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 52 optimal weight: 0.8980 chunk 76 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 90 optimal weight: 10.0000 chunk 81 optimal weight: 0.6980 chunk 85 optimal weight: 9.9990 chunk 45 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 183 GLN B 142 ASN B 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3856 r_free = 0.3856 target = 0.119516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.094045 restraints weight = 21138.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.096072 restraints weight = 12498.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.097435 restraints weight = 8532.375| |-----------------------------------------------------------------------------| r_work (final): 0.3497 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3497 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3497 r_free = 0.3497 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3497 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9531 Z= 0.154 Angle : 0.596 7.779 13316 Z= 0.332 Chirality : 0.041 0.154 1461 Planarity : 0.005 0.052 1363 Dihedral : 21.578 140.990 2059 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 1.81 % Allowed : 13.55 % Favored : 84.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.29), residues: 861 helix: 1.13 (0.27), residues: 377 sheet: -0.47 (0.48), residues: 109 loop : -1.36 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 124 HIS 0.004 0.001 HIS A 160 PHE 0.013 0.002 PHE A 352 TYR 0.019 0.001 TYR B 21 ARG 0.003 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04927 ( 309) hydrogen bonds : angle 4.03534 ( 866) covalent geometry : bond 0.00345 ( 9531) covalent geometry : angle 0.59605 (13316) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 71 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: A 365 MET cc_start: 0.6151 (mmm) cc_final: 0.5832 (mmm) REVERT: A 413 GLU cc_start: 0.8218 (tm-30) cc_final: 0.7753 (tp30) REVERT: B 115 ASP cc_start: 0.6426 (m-30) cc_final: 0.6026 (m-30) outliers start: 14 outliers final: 9 residues processed: 80 average time/residue: 0.1809 time to fit residues: 21.5943 Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 350 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 92 optimal weight: 9.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 1.9990 chunk 83 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 1.9990 chunk 75 optimal weight: 0.6980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 53 GLN B 142 ASN B 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3879 r_free = 0.3879 target = 0.120999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.095630 restraints weight = 20911.522| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.097799 restraints weight = 12073.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099271 restraints weight = 8075.396| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3525 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3525 r_free = 0.3525 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3525 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9531 Z= 0.130 Angle : 0.568 8.172 13316 Z= 0.317 Chirality : 0.040 0.149 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.599 141.415 2059 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.81 % Allowed : 15.23 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.13 (0.29), residues: 861 helix: 1.19 (0.27), residues: 380 sheet: -0.38 (0.48), residues: 109 loop : -1.36 (0.32), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 PHE 0.011 0.001 PHE A 77 TYR 0.019 0.001 TYR B 21 ARG 0.002 0.000 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.04420 ( 309) hydrogen bonds : angle 3.83341 ( 866) covalent geometry : bond 0.00283 ( 9531) covalent geometry : angle 0.56840 (13316) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 73 time to evaluate : 2.015 Fit side-chains REVERT: A 365 MET cc_start: 0.6091 (mmm) cc_final: 0.5787 (mmm) REVERT: A 413 GLU cc_start: 0.8230 (tm-30) cc_final: 0.7801 (tp30) REVERT: B 62 GLN cc_start: 0.6929 (tm-30) cc_final: 0.6073 (tp40) REVERT: B 115 ASP cc_start: 0.6392 (m-30) cc_final: 0.5974 (m-30) REVERT: B 339 SER cc_start: 0.8750 (OUTLIER) cc_final: 0.8260 (t) outliers start: 14 outliers final: 8 residues processed: 84 average time/residue: 0.4020 time to fit residues: 51.1304 Evaluate side-chains 74 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 1.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 299 ASN Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 34 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 6 optimal weight: 0.4980 chunk 60 optimal weight: 0.9990 chunk 71 optimal weight: 8.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.2980 chunk 84 optimal weight: 0.0070 chunk 59 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 overall best weight: 0.5400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 80 GLN A 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.123265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.097751 restraints weight = 20601.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.099978 restraints weight = 11915.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.101435 restraints weight = 7965.844| |-----------------------------------------------------------------------------| r_work (final): 0.3559 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3560 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3560 r_free = 0.3560 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3560 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7316 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9531 Z= 0.120 Angle : 0.547 8.439 13316 Z= 0.304 Chirality : 0.039 0.144 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.688 142.024 2059 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 7.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 1.55 % Allowed : 16.65 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.09 (0.29), residues: 861 helix: 1.43 (0.28), residues: 377 sheet: -0.22 (0.48), residues: 109 loop : -1.29 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 124 HIS 0.002 0.001 HIS B 110 PHE 0.010 0.001 PHE A 77 TYR 0.018 0.001 TYR B 21 ARG 0.003 0.000 ARG B 271 Details of bonding type rmsd hydrogen bonds : bond 0.04059 ( 309) hydrogen bonds : angle 3.68622 ( 866) covalent geometry : bond 0.00256 ( 9531) covalent geometry : angle 0.54691 (13316) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 74 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 312 ILE cc_start: 0.8668 (mp) cc_final: 0.8452 (mp) REVERT: A 365 MET cc_start: 0.6091 (mmm) cc_final: 0.5764 (mmm) REVERT: A 413 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7882 (tp30) REVERT: B 115 ASP cc_start: 0.6360 (m-30) cc_final: 0.5980 (m-30) REVERT: B 195 TYR cc_start: 0.7063 (m-80) cc_final: 0.6807 (m-10) REVERT: B 339 SER cc_start: 0.8681 (OUTLIER) cc_final: 0.8154 (t) REVERT: B 365 MET cc_start: 0.8490 (mmm) cc_final: 0.8093 (mmm) outliers start: 12 outliers final: 7 residues processed: 82 average time/residue: 0.2496 time to fit residues: 29.5791 Evaluate side-chains 78 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 76 optimal weight: 2.9990 chunk 48 optimal weight: 5.9990 chunk 83 optimal weight: 0.0000 chunk 85 optimal weight: 0.0370 chunk 6 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 92 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 overall best weight: 1.1266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.122435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.096768 restraints weight = 20877.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.098924 restraints weight = 12077.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.100404 restraints weight = 8113.389| |-----------------------------------------------------------------------------| r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3546 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3546 r_free = 0.3546 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3546 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9531 Z= 0.127 Angle : 0.556 8.100 13316 Z= 0.308 Chirality : 0.040 0.201 1461 Planarity : 0.005 0.048 1363 Dihedral : 21.732 141.892 2059 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.68 % Allowed : 17.68 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.14 (0.29), residues: 861 helix: 1.47 (0.28), residues: 377 sheet: -0.17 (0.49), residues: 109 loop : -1.27 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 PHE 0.010 0.001 PHE A 121 TYR 0.020 0.001 TYR B 21 ARG 0.004 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04123 ( 309) hydrogen bonds : angle 3.69169 ( 866) covalent geometry : bond 0.00279 ( 9531) covalent geometry : angle 0.55576 (13316) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 72 time to evaluate : 1.525 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.5871 (mmpt) cc_final: 0.5036 (tmtt) REVERT: A 312 ILE cc_start: 0.8633 (mp) cc_final: 0.8375 (mp) REVERT: A 365 MET cc_start: 0.6094 (mmm) cc_final: 0.5880 (mmm) REVERT: A 413 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7868 (tp30) REVERT: B 115 ASP cc_start: 0.6354 (m-30) cc_final: 0.5969 (m-30) REVERT: B 339 SER cc_start: 0.8692 (OUTLIER) cc_final: 0.8190 (t) outliers start: 13 outliers final: 10 residues processed: 81 average time/residue: 0.3372 time to fit residues: 40.9167 Evaluate side-chains 81 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 70 time to evaluate : 0.946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Chi-restraints excluded: chain B residue 308 SER Chi-restraints excluded: chain B residue 339 SER Chi-restraints excluded: chain B residue 349 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 66 optimal weight: 7.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 39 optimal weight: 9.9990 chunk 71 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 76 optimal weight: 5.9990 chunk 29 optimal weight: 0.5980 chunk 20 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN A 256 ASN ** B 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.118112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.092646 restraints weight = 21462.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.094691 restraints weight = 12526.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.096098 restraints weight = 8502.919| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3467 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3467 r_free = 0.3467 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3467 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7471 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9531 Z= 0.196 Angle : 0.646 7.478 13316 Z= 0.355 Chirality : 0.043 0.231 1461 Planarity : 0.005 0.050 1363 Dihedral : 22.025 140.510 2059 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.81 % Allowed : 18.71 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.21 (0.29), residues: 861 helix: 1.14 (0.27), residues: 378 sheet: -0.54 (0.48), residues: 108 loop : -1.34 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 124 HIS 0.005 0.001 HIS A 160 PHE 0.018 0.002 PHE A 352 TYR 0.021 0.002 TYR B 21 ARG 0.004 0.001 ARG A 343 Details of bonding type rmsd hydrogen bonds : bond 0.05082 ( 309) hydrogen bonds : angle 4.08686 ( 866) covalent geometry : bond 0.00450 ( 9531) covalent geometry : angle 0.64610 (13316) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.999 Fit side-chains REVERT: A 307 PHE cc_start: 0.8103 (OUTLIER) cc_final: 0.7488 (t80) REVERT: B 38 LYS cc_start: 0.7527 (mmtt) cc_final: 0.7324 (mmtt) REVERT: B 115 ASP cc_start: 0.6449 (m-30) cc_final: 0.6049 (m-30) outliers start: 14 outliers final: 8 residues processed: 77 average time/residue: 0.1867 time to fit residues: 21.5484 Evaluate side-chains 75 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 66 time to evaluate : 0.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 9.9990 chunk 74 optimal weight: 4.9990 chunk 43 optimal weight: 0.0050 chunk 28 optimal weight: 0.9980 overall best weight: 1.1598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.121681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095853 restraints weight = 20947.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097985 restraints weight = 12141.039| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.099444 restraints weight = 8196.790| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3521 r_free = 0.3521 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9531 Z= 0.131 Angle : 0.576 7.680 13316 Z= 0.319 Chirality : 0.040 0.183 1461 Planarity : 0.005 0.049 1363 Dihedral : 21.992 140.642 2059 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 1.29 % Allowed : 19.35 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: -0.01 (0.29), residues: 861 helix: 1.37 (0.27), residues: 377 sheet: -0.40 (0.48), residues: 109 loop : -1.33 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.004 0.001 HIS B 110 PHE 0.011 0.001 PHE A 119 TYR 0.021 0.001 TYR A 336 ARG 0.003 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04253 ( 309) hydrogen bonds : angle 3.76989 ( 866) covalent geometry : bond 0.00289 ( 9531) covalent geometry : angle 0.57624 (13316) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.878 Fit side-chains revert: symmetry clash REVERT: A 307 PHE cc_start: 0.7874 (OUTLIER) cc_final: 0.7282 (t80) REVERT: A 413 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7826 (tp30) REVERT: B 38 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7329 (mmtt) REVERT: B 115 ASP cc_start: 0.6568 (m-30) cc_final: 0.6149 (m-30) outliers start: 10 outliers final: 8 residues processed: 75 average time/residue: 0.1892 time to fit residues: 21.2239 Evaluate side-chains 76 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 67 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.0370 chunk 84 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 26 optimal weight: 0.0000 chunk 53 optimal weight: 1.9990 overall best weight: 0.8066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.122576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.096647 restraints weight = 21072.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.098828 restraints weight = 12199.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.100298 restraints weight = 8191.474| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3538 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3538 r_free = 0.3538 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3538 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9531 Z= 0.126 Angle : 0.575 7.768 13316 Z= 0.316 Chirality : 0.040 0.178 1461 Planarity : 0.005 0.049 1363 Dihedral : 21.960 140.738 2059 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 1.29 % Allowed : 19.35 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.07 (0.29), residues: 861 helix: 1.45 (0.27), residues: 377 sheet: -0.33 (0.48), residues: 109 loop : -1.31 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 124 HIS 0.004 0.001 HIS A 145 PHE 0.011 0.001 PHE A 119 TYR 0.020 0.001 TYR B 21 ARG 0.004 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04134 ( 309) hydrogen bonds : angle 3.72260 ( 866) covalent geometry : bond 0.00277 ( 9531) covalent geometry : angle 0.57465 (13316) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1722 Ramachandran restraints generated. 861 Oldfield, 0 Emsley, 861 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 70 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 307 PHE cc_start: 0.7846 (OUTLIER) cc_final: 0.7310 (t80) REVERT: A 413 GLU cc_start: 0.8153 (tm-30) cc_final: 0.7905 (tp30) REVERT: B 38 LYS cc_start: 0.7513 (mmtt) cc_final: 0.7297 (mmtt) REVERT: B 61 GLU cc_start: 0.8385 (tm-30) cc_final: 0.7861 (tm-30) REVERT: B 115 ASP cc_start: 0.6472 (m-30) cc_final: 0.6114 (m-30) REVERT: B 365 MET cc_start: 0.8461 (mmm) cc_final: 0.7935 (mmm) outliers start: 10 outliers final: 9 residues processed: 75 average time/residue: 0.1986 time to fit residues: 21.8946 Evaluate side-chains 77 residues out of total 773 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 142 ASN Chi-restraints excluded: chain A residue 251 SER Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 320 MET Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain B residue 72 ILE Chi-restraints excluded: chain B residue 110 HIS Chi-restraints excluded: chain B residue 142 ASN Chi-restraints excluded: chain B residue 145 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 88 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 90 optimal weight: 10.0000 chunk 73 optimal weight: 0.9990 chunk 84 optimal weight: 0.8980 chunk 52 optimal weight: 0.7980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 142 ASN B 142 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.121718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.095841 restraints weight = 20927.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.097959 restraints weight = 12186.925| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.099379 restraints weight = 8252.369| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3522 r_free = 0.3522 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 9531 Z= 0.139 Angle : 0.587 8.988 13316 Z= 0.321 Chirality : 0.040 0.181 1461 Planarity : 0.005 0.050 1363 Dihedral : 21.982 140.470 2059 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.68 % Allowed : 19.35 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.06 (0.29), residues: 861 helix: 1.44 (0.28), residues: 377 sheet: -0.40 (0.48), residues: 109 loop : -1.29 (0.32), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 124 HIS 0.003 0.001 HIS B 110 PHE 0.013 0.002 PHE A 77 TYR 0.020 0.001 TYR B 21 ARG 0.002 0.000 ARG B 138 Details of bonding type rmsd hydrogen bonds : bond 0.04231 ( 309) hydrogen bonds : angle 3.77073 ( 866) covalent geometry : bond 0.00312 ( 9531) covalent geometry : angle 0.58665 (13316) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4126.92 seconds wall clock time: 75 minutes 41.09 seconds (4541.09 seconds total)