Starting phenix.real_space_refine on Sat Jun 14 20:55:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.map" model { file = "/net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9by0_45016/06_2025/9by0_45016.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 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: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10641 2.51 5 N 2712 2.21 5 O 3216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.48, per 1000 atoms: 0.57 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 137.904, 143.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 87 16.00 P 16 15.00 Mg 2 11.99 O 3216 8.00 N 2712 7.00 C 10641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 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: 4.30 Conformation dependent library (CDL) restraints added in 2.2 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.260A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.787A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.525A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.527A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.662A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.231A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.567A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.633A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.256A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.021A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.817A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.879A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.467A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2664 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: 5.29 Time building geometry restraints manager: 4.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 5051 1.34 - 1.46: 3090 1.46 - 1.58: 8708 1.58 - 1.70: 25 1.70 - 1.82: 164 Bond restraints: 17038 Sorted by residual: bond pdb=" CA VAL C 125 " pdb=" CB VAL C 125 " ideal model delta sigma weight residual 1.540 1.601 -0.061 1.25e-02 6.40e+03 2.37e+01 bond pdb=" CA ILE D 138 " pdb=" CB ILE D 138 " ideal model delta sigma weight residual 1.539 1.578 -0.038 1.20e-02 6.94e+03 1.01e+01 bond pdb=" CA VAL C 250 " pdb=" CB VAL C 250 " ideal model delta sigma weight residual 1.542 1.575 -0.032 1.08e-02 8.57e+03 8.94e+00 bond pdb=" CA ILE D 35 " pdb=" CB ILE D 35 " ideal model delta sigma weight residual 1.537 1.569 -0.032 1.17e-02 7.31e+03 7.60e+00 bond pdb=" CA VAL D 203 " pdb=" CB VAL D 203 " ideal model delta sigma weight residual 1.540 1.573 -0.032 1.25e-02 6.40e+03 6.69e+00 ... (remaining 17033 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.64: 22885 3.64 - 7.28: 126 7.28 - 10.92: 7 10.92 - 14.56: 1 14.56 - 18.20: 1 Bond angle restraints: 23020 Sorted by residual: angle pdb=" CA VAL E 69 " pdb=" C VAL E 69 " pdb=" N MET E 70 " ideal model delta sigma weight residual 116.36 105.10 11.26 9.70e-01 1.06e+00 1.35e+02 angle pdb=" O VAL E 69 " pdb=" C VAL E 69 " pdb=" N MET E 70 " ideal model delta sigma weight residual 122.66 133.31 -10.65 1.15e+00 7.56e-01 8.58e+01 angle pdb=" C VAL E 69 " pdb=" N MET E 70 " pdb=" CA MET E 70 " ideal model delta sigma weight residual 121.64 139.84 -18.20 2.13e+00 2.20e-01 7.30e+01 angle pdb=" N PHE B 624 " pdb=" CA PHE B 624 " pdb=" C PHE B 624 " ideal model delta sigma weight residual 113.01 119.15 -6.14 1.20e+00 6.94e-01 2.62e+01 angle pdb=" CB HIS E 103 " pdb=" CG HIS E 103 " pdb=" CD2 HIS E 103 " ideal model delta sigma weight residual 131.20 125.31 5.89 1.30e+00 5.92e-01 2.05e+01 ... (remaining 23015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.73: 9644 29.73 - 59.45: 545 59.45 - 89.18: 60 89.18 - 118.91: 3 118.91 - 148.64: 4 Dihedral angle restraints: 10256 sinusoidal: 4264 harmonic: 5992 Sorted by residual: dihedral pdb=" CB CYS B 170 " pdb=" SG CYS B 170 " pdb=" SG CYS B 409 " pdb=" CB CYS B 409 " ideal model delta sinusoidal sigma weight residual -86.00 -170.27 84.27 1 1.00e+01 1.00e-02 8.64e+01 dihedral pdb=" C PHE B 624 " pdb=" N PHE B 624 " pdb=" CA PHE B 624 " pdb=" CB PHE B 624 " ideal model delta harmonic sigma weight residual -122.60 -139.39 16.79 0 2.50e+00 1.60e-01 4.51e+01 dihedral pdb=" C2 TTP A 801 " pdb=" C1' TTP A 801 " pdb=" N1 TTP A 801 " pdb=" O4' TTP A 801 " ideal model delta sinusoidal sigma weight residual 301.68 153.05 148.64 1 2.00e+01 2.50e-03 4.45e+01 ... (remaining 10253 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.145: 2392 0.145 - 0.289: 67 0.289 - 0.433: 3 0.433 - 0.578: 1 0.578 - 0.722: 1 Chirality restraints: 2464 Sorted by residual: chirality pdb=" CA PHE B 624 " pdb=" N PHE B 624 " pdb=" C PHE B 624 " pdb=" CB PHE B 624 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.30e+01 chirality pdb=" CA ASN C 98 " pdb=" N ASN C 98 " pdb=" C ASN C 98 " pdb=" CB ASN C 98 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.47e+00 chirality pdb=" CA TYR C 169 " pdb=" N TYR C 169 " pdb=" C TYR C 169 " pdb=" CB TYR C 169 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.61e+00 ... (remaining 2461 not shown) Planarity restraints: 2931 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 624 " -0.084 2.00e-02 2.50e+03 5.98e-02 6.27e+01 pdb=" CG PHE B 624 " 0.120 2.00e-02 2.50e+03 pdb=" CD1 PHE B 624 " 0.033 2.00e-02 2.50e+03 pdb=" CD2 PHE B 624 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE B 624 " -0.042 2.00e-02 2.50e+03 pdb=" CE2 PHE B 624 " 0.007 2.00e-02 2.50e+03 pdb=" CZ PHE B 624 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 25 " 0.077 2.00e-02 2.50e+03 3.68e-02 3.39e+01 pdb=" CG TRP E 25 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 TRP E 25 " -0.040 2.00e-02 2.50e+03 pdb=" CD2 TRP E 25 " -0.034 2.00e-02 2.50e+03 pdb=" NE1 TRP E 25 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP E 25 " -0.007 2.00e-02 2.50e+03 pdb=" CE3 TRP E 25 " -0.040 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 25 " 0.035 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 25 " -0.014 2.00e-02 2.50e+03 pdb=" CH2 TRP E 25 " 0.035 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 58 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.40e+00 pdb=" CG ASP E 58 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP E 58 " 0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 58 " 0.018 2.00e-02 2.50e+03 ... (remaining 2928 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 126 2.51 - 3.11: 12015 3.11 - 3.70: 27825 3.70 - 4.30: 42565 4.30 - 4.90: 68561 Nonbonded interactions: 151092 Sorted by model distance: nonbonded pdb=" OE2 GLU D 97 " pdb="MN MN D 401 " model vdw 1.912 2.320 nonbonded pdb=" OE2 GLU C 97 " pdb="MN MN C 401 " model vdw 1.960 2.320 nonbonded pdb=" OE2 GLU C 164 " pdb="MN MN C 401 " model vdw 1.966 2.320 nonbonded pdb=" OE1 GLU D 97 " pdb="MN MN D 402 " model vdw 1.990 2.320 nonbonded pdb=" OD1 ASP C 66 " pdb="MN MN C 402 " model vdw 2.030 2.320 ... (remaining 151087 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 6 through 688 or resid 803 through 804)) selection = (chain 'B' and (resid 6 through 688 or resid 803 through 804)) } ncs_group { reference = chain 'C' selection = chain 'D' } 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: 1.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.740 Check model and map are aligned: 0.140 Set scattering table: 0.150 Process input model: 37.240 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 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 : 0.008 0.629 17041 Z= 0.416 Angle : 0.841 18.197 23026 Z= 0.527 Chirality : 0.061 0.722 2464 Planarity : 0.004 0.060 2931 Dihedral : 17.534 148.635 6399 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 16.27 % Favored : 82.34 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % 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: 0.56 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.31 (0.37), residues: 179 loop : 0.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 PHE 0.120 0.003 PHE B 624 TYR 0.029 0.002 TYR E 67 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.16741 ( 912) hydrogen bonds : angle 6.70349 ( 2664) SS BOND : bond 0.36331 ( 3) SS BOND : angle 6.07971 ( 6) covalent geometry : bond 0.00602 (17038) covalent geometry : angle 0.83524 (23020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 943 time to evaluate : 1.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.8664 (t) cc_final: 0.8425 (p) REVERT: A 68 PHE cc_start: 0.7989 (p90) cc_final: 0.7642 (p90) REVERT: A 171 PHE cc_start: 0.8288 (m-80) cc_final: 0.7976 (m-80) REVERT: A 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8660 (t0) REVERT: A 367 VAL cc_start: 0.8707 (m) cc_final: 0.8307 (p) REVERT: A 378 PHE cc_start: 0.8293 (p90) cc_final: 0.7930 (p90) REVERT: A 483 GLU cc_start: 0.8151 (mp0) cc_final: 0.7913 (mp0) REVERT: A 655 THR cc_start: 0.9457 (m) cc_final: 0.9200 (t) REVERT: B 17 MET cc_start: 0.7011 (mmm) cc_final: 0.6213 (mmm) REVERT: B 41 ILE cc_start: 0.8797 (mm) cc_final: 0.8316 (mt) REVERT: B 46 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (m) REVERT: B 51 LEU cc_start: 0.7905 (tp) cc_final: 0.7640 (tp) REVERT: B 127 LEU cc_start: 0.9293 (mt) cc_final: 0.9060 (mt) REVERT: B 129 PHE cc_start: 0.7800 (m-10) cc_final: 0.7473 (m-80) REVERT: B 177 ASP cc_start: 0.8336 (t0) cc_final: 0.7989 (t0) REVERT: B 204 SER cc_start: 0.8620 (m) cc_final: 0.8397 (t) REVERT: B 230 LEU cc_start: 0.9308 (mt) cc_final: 0.9080 (mt) REVERT: B 315 ASP cc_start: 0.8578 (p0) cc_final: 0.8314 (t0) REVERT: B 322 MET cc_start: 0.7356 (mmm) cc_final: 0.6949 (mmm) REVERT: B 349 LEU cc_start: 0.8462 (mt) cc_final: 0.8151 (mp) REVERT: B 364 VAL cc_start: 0.8818 (t) cc_final: 0.8598 (t) REVERT: B 384 GLU cc_start: 0.8215 (pp20) cc_final: 0.7610 (pm20) REVERT: B 385 VAL cc_start: 0.8660 (t) cc_final: 0.8392 (t) REVERT: B 417 LEU cc_start: 0.8368 (tp) cc_final: 0.8053 (tp) REVERT: B 500 ILE cc_start: 0.9353 (mt) cc_final: 0.8767 (mt) REVERT: B 531 TYR cc_start: 0.6004 (m-80) cc_final: 0.5682 (m-80) REVERT: B 550 MET cc_start: 0.7101 (mtm) cc_final: 0.6594 (mtp) REVERT: B 574 TYR cc_start: 0.8035 (m-80) cc_final: 0.7820 (m-80) REVERT: B 576 LEU cc_start: 0.8710 (mt) cc_final: 0.8327 (mt) REVERT: B 644 ILE cc_start: 0.8828 (mt) cc_final: 0.8593 (mt) REVERT: B 687 THR cc_start: 0.7230 (p) cc_final: 0.6959 (p) REVERT: C 89 VAL cc_start: 0.6220 (t) cc_final: 0.5263 (t) REVERT: C 101 HIS cc_start: 0.5472 (m170) cc_final: 0.4826 (m-70) REVERT: C 131 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6050 (tp) REVERT: C 153 LEU cc_start: 0.7009 (tp) cc_final: 0.6724 (tp) REVERT: C 163 LEU cc_start: 0.6154 (tt) cc_final: 0.5807 (tp) REVERT: C 268 LEU cc_start: 0.4343 (mt) cc_final: 0.4057 (mt) REVERT: D 185 MET cc_start: 0.6866 (mmm) cc_final: 0.6551 (tpp) REVERT: D 265 ASN cc_start: 0.4744 (m-40) cc_final: 0.4472 (m110) REVERT: E 25 TRP cc_start: 0.8230 (p-90) cc_final: 0.7924 (p-90) REVERT: E 78 LEU cc_start: 0.6579 (mp) cc_final: 0.5543 (tt) outliers start: 25 outliers final: 3 residues processed: 948 average time/residue: 0.3195 time to fit residues: 441.8010 Evaluate side-chains 637 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 632 time to evaluate : 1.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 61 ASN B 191 GLN B 304 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 216 GLN C 263 ASN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.129830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.092213 restraints weight = 41535.700| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.095824 restraints weight = 21440.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.098243 restraints weight = 13389.477| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3239 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3239 r_free = 0.3239 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 = 0.3237 r_free = 0.3237 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3237 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7394 moved from start: 0.4584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 17041 Z= 0.242 Angle : 0.714 15.452 23026 Z= 0.375 Chirality : 0.045 0.187 2464 Planarity : 0.005 0.049 2931 Dihedral : 10.723 150.951 2325 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.34 % Allowed : 2.91 % Favored : 96.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.17 (0.18), residues: 2012 helix: 1.21 (0.15), residues: 1158 sheet: -0.14 (0.39), residues: 155 loop : 0.48 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 623 HIS 0.009 0.001 HIS B 438 PHE 0.037 0.002 PHE C 168 TYR 0.028 0.002 TYR D 174 ARG 0.010 0.001 ARG A 235 Details of bonding type rmsd hydrogen bonds : bond 0.04730 ( 912) hydrogen bonds : angle 5.16598 ( 2664) SS BOND : bond 0.00408 ( 3) SS BOND : angle 7.77520 ( 6) covalent geometry : bond 0.00516 (17038) covalent geometry : angle 0.70311 (23020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 737 time to evaluate : 2.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 LEU cc_start: 0.9555 (tp) cc_final: 0.9340 (tp) REVERT: A 119 GLU cc_start: 0.8539 (mp0) cc_final: 0.8235 (mm-30) REVERT: A 147 GLN cc_start: 0.8623 (tp-100) cc_final: 0.7900 (tp40) REVERT: A 195 LEU cc_start: 0.9394 (mt) cc_final: 0.9147 (mt) REVERT: A 223 VAL cc_start: 0.9500 (m) cc_final: 0.9191 (p) REVERT: A 224 VAL cc_start: 0.9492 (m) cc_final: 0.9260 (m) REVERT: A 227 MET cc_start: 0.9319 (mtm) cc_final: 0.9118 (mtm) REVERT: A 256 ARG cc_start: 0.8400 (ttp80) cc_final: 0.7570 (ttp80) REVERT: A 301 PHE cc_start: 0.8972 (m-80) cc_final: 0.8749 (m-80) REVERT: A 320 ASN cc_start: 0.8249 (m-40) cc_final: 0.8036 (m110) REVERT: A 338 ASN cc_start: 0.9554 (t0) cc_final: 0.7872 (t0) REVERT: A 341 LYS cc_start: 0.9691 (mmtp) cc_final: 0.9376 (mmtp) REVERT: A 346 LEU cc_start: 0.9537 (mt) cc_final: 0.9324 (mt) REVERT: A 360 PHE cc_start: 0.8507 (m-80) cc_final: 0.7952 (m-80) REVERT: A 367 VAL cc_start: 0.9511 (m) cc_final: 0.9218 (p) REVERT: A 421 GLU cc_start: 0.8209 (pp20) cc_final: 0.7877 (pp20) REVERT: A 453 ARG cc_start: 0.9243 (ttt-90) cc_final: 0.8814 (ttt-90) REVERT: A 466 MET cc_start: 0.8384 (ptt) cc_final: 0.7992 (ptt) REVERT: A 475 ASN cc_start: 0.8392 (m110) cc_final: 0.8039 (m110) REVERT: A 501 GLN cc_start: 0.9288 (tt0) cc_final: 0.8088 (tm-30) REVERT: A 505 GLU cc_start: 0.8537 (pt0) cc_final: 0.7765 (pt0) REVERT: A 509 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8452 (tm-30) REVERT: A 512 GLU cc_start: 0.8059 (pm20) cc_final: 0.7672 (pm20) REVERT: A 518 GLU cc_start: 0.8940 (pp20) cc_final: 0.8647 (pp20) REVERT: A 528 PHE cc_start: 0.8462 (m-10) cc_final: 0.8173 (m-80) REVERT: A 558 TRP cc_start: 0.9023 (m100) cc_final: 0.8359 (m100) REVERT: A 571 TYR cc_start: 0.8516 (t80) cc_final: 0.8142 (t80) REVERT: A 615 MET cc_start: 0.8863 (mmm) cc_final: 0.8518 (mmm) REVERT: A 639 ASP cc_start: 0.8910 (m-30) cc_final: 0.8595 (m-30) REVERT: A 655 THR cc_start: 0.8991 (m) cc_final: 0.8602 (t) REVERT: A 658 LEU cc_start: 0.9586 (mp) cc_final: 0.9349 (mp) REVERT: B 127 LEU cc_start: 0.9796 (mt) cc_final: 0.9550 (mm) REVERT: B 135 GLU cc_start: 0.9172 (mp0) cc_final: 0.8843 (pm20) REVERT: B 147 GLN cc_start: 0.9049 (mt0) cc_final: 0.8009 (mm-40) REVERT: B 150 GLN cc_start: 0.9377 (tp-100) cc_final: 0.8865 (tp-100) REVERT: B 156 PHE cc_start: 0.9276 (t80) cc_final: 0.9027 (t80) REVERT: B 186 ILE cc_start: 0.9677 (mt) cc_final: 0.9350 (mt) REVERT: B 190 MET cc_start: 0.9365 (mtm) cc_final: 0.8882 (mtm) REVERT: B 216 VAL cc_start: 0.9059 (t) cc_final: 0.8857 (p) REVERT: B 227 MET cc_start: 0.9206 (mtp) cc_final: 0.8960 (mtp) REVERT: B 256 ARG cc_start: 0.8426 (tmt170) cc_final: 0.8081 (ttp80) REVERT: B 257 ASP cc_start: 0.8466 (m-30) cc_final: 0.7681 (m-30) REVERT: B 260 ASP cc_start: 0.9271 (m-30) cc_final: 0.9050 (p0) REVERT: B 286 ASP cc_start: 0.8438 (m-30) cc_final: 0.8216 (m-30) REVERT: B 317 MET cc_start: 0.8852 (mtp) cc_final: 0.8484 (mtt) REVERT: B 322 MET cc_start: 0.8625 (mmm) cc_final: 0.8384 (mmm) REVERT: B 348 MET cc_start: 0.9063 (ppp) cc_final: 0.8467 (ppp) REVERT: B 349 LEU cc_start: 0.9373 (mt) cc_final: 0.8868 (mt) REVERT: B 375 LYS cc_start: 0.8799 (mmmm) cc_final: 0.8442 (mmmm) REVERT: B 402 GLU cc_start: 0.8081 (mp0) cc_final: 0.7706 (mp0) REVERT: B 458 MET cc_start: 0.8980 (mmp) cc_final: 0.8252 (mmp) REVERT: B 510 LYS cc_start: 0.9378 (mmtm) cc_final: 0.9150 (mmtm) REVERT: B 515 ASP cc_start: 0.8977 (m-30) cc_final: 0.8538 (p0) REVERT: B 546 LEU cc_start: 0.9455 (mm) cc_final: 0.9139 (mp) REVERT: B 558 TRP cc_start: 0.8779 (m100) cc_final: 0.8309 (m100) REVERT: B 586 TYR cc_start: 0.8992 (m-80) cc_final: 0.8564 (m-80) REVERT: B 634 MET cc_start: 0.8164 (mmp) cc_final: 0.7841 (mmt) REVERT: B 656 LEU cc_start: 0.9311 (mt) cc_final: 0.9015 (mt) REVERT: C 17 PHE cc_start: 0.9028 (p90) cc_final: 0.8551 (p90) REVERT: C 23 ASN cc_start: 0.9697 (m-40) cc_final: 0.9437 (m-40) REVERT: C 56 MET cc_start: 0.1044 (ptm) cc_final: 0.0727 (ttp) REVERT: C 74 MET cc_start: 0.9423 (mpp) cc_final: 0.9060 (mpp) REVERT: C 154 PHE cc_start: 0.9256 (t80) cc_final: 0.8766 (t80) REVERT: C 157 MET cc_start: 0.9394 (mtm) cc_final: 0.8946 (ptt) REVERT: C 163 LEU cc_start: 0.9121 (tt) cc_final: 0.8818 (tp) REVERT: C 174 TYR cc_start: 0.8882 (t80) cc_final: 0.8542 (t80) REVERT: C 207 LEU cc_start: 0.9165 (mt) cc_final: 0.8902 (mt) REVERT: C 212 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.7907 (mm) REVERT: C 226 GLU cc_start: 0.8743 (tt0) cc_final: 0.8530 (tt0) REVERT: C 227 PHE cc_start: 0.8809 (t80) cc_final: 0.8597 (t80) REVERT: C 233 ASN cc_start: 0.9306 (m-40) cc_final: 0.8986 (m-40) REVERT: C 320 PHE cc_start: 0.8824 (m-80) cc_final: 0.8296 (m-80) REVERT: D 16 ASP cc_start: 0.6744 (t0) cc_final: 0.6469 (t0) REVERT: D 109 PHE cc_start: 0.8755 (m-10) cc_final: 0.8467 (m-80) REVERT: D 115 THR cc_start: 0.8511 (m) cc_final: 0.8292 (p) REVERT: D 119 ASN cc_start: 0.8534 (m110) cc_final: 0.8130 (m-40) REVERT: D 128 ASN cc_start: 0.8948 (t0) cc_final: 0.8056 (t0) REVERT: D 133 LYS cc_start: 0.8207 (ttmt) cc_final: 0.7987 (tptp) REVERT: D 216 GLN cc_start: 0.7223 (mt0) cc_final: 0.6899 (mt0) REVERT: E 25 TRP cc_start: 0.8182 (p-90) cc_final: 0.7775 (p-90) REVERT: E 46 MET cc_start: 0.8010 (tpp) cc_final: 0.6887 (mpp) REVERT: E 70 MET cc_start: 0.8179 (mmp) cc_final: 0.7837 (mpp) outliers start: 6 outliers final: 1 residues processed: 739 average time/residue: 0.2890 time to fit residues: 319.1643 Evaluate side-chains 594 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 592 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 0.1980 chunk 81 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 115 optimal weight: 2.9990 chunk 132 optimal weight: 1.9990 chunk 118 optimal weight: 0.8980 chunk 144 optimal weight: 5.9990 chunk 112 optimal weight: 0.9990 chunk 179 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 365 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 44 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN D 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.133397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.094859 restraints weight = 41187.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.098660 restraints weight = 21004.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.101058 restraints weight = 12975.607| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 17041 Z= 0.144 Angle : 0.607 8.362 23026 Z= 0.316 Chirality : 0.044 0.317 2464 Planarity : 0.004 0.051 2931 Dihedral : 10.382 144.072 2325 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.06 % Allowed : 1.90 % Favored : 98.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.18), residues: 2012 helix: 1.29 (0.15), residues: 1153 sheet: -0.13 (0.40), residues: 165 loop : 0.44 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 623 HIS 0.008 0.001 HIS B 438 PHE 0.028 0.002 PHE A 492 TYR 0.025 0.002 TYR B 574 ARG 0.008 0.001 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.04195 ( 912) hydrogen bonds : angle 4.89484 ( 2664) SS BOND : bond 0.00311 ( 3) SS BOND : angle 3.68682 ( 6) covalent geometry : bond 0.00316 (17038) covalent geometry : angle 0.60377 (23020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 731 time to evaluate : 1.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 GLU cc_start: 0.9119 (mp0) cc_final: 0.8898 (mm-30) REVERT: A 115 LEU cc_start: 0.8652 (mt) cc_final: 0.8337 (mp) REVERT: A 158 ASN cc_start: 0.8857 (m-40) cc_final: 0.8569 (m110) REVERT: A 162 LYS cc_start: 0.9307 (tmtt) cc_final: 0.9084 (tmmt) REVERT: A 187 ASP cc_start: 0.8682 (t70) cc_final: 0.8306 (t0) REVERT: A 209 LYS cc_start: 0.9103 (tttm) cc_final: 0.8850 (tttm) REVERT: A 223 VAL cc_start: 0.9530 (m) cc_final: 0.9204 (p) REVERT: A 254 PHE cc_start: 0.8841 (m-80) cc_final: 0.8427 (m-80) REVERT: A 256 ARG cc_start: 0.9147 (tmt-80) cc_final: 0.8577 (tmt-80) REVERT: A 262 LEU cc_start: 0.9528 (mt) cc_final: 0.9300 (mt) REVERT: A 286 ASP cc_start: 0.8725 (m-30) cc_final: 0.8439 (m-30) REVERT: A 290 GLU cc_start: 0.9175 (tm-30) cc_final: 0.8772 (tm-30) REVERT: A 291 LEU cc_start: 0.9521 (mm) cc_final: 0.9255 (mm) REVERT: A 301 PHE cc_start: 0.8977 (m-80) cc_final: 0.8675 (m-80) REVERT: A 348 MET cc_start: 0.8882 (ptm) cc_final: 0.8591 (ptm) REVERT: A 362 ASP cc_start: 0.8471 (m-30) cc_final: 0.8165 (m-30) REVERT: A 367 VAL cc_start: 0.9531 (m) cc_final: 0.9264 (p) REVERT: A 390 GLN cc_start: 0.8581 (mt0) cc_final: 0.8269 (mt0) REVERT: A 403 ILE cc_start: 0.9203 (mp) cc_final: 0.8723 (mp) REVERT: A 417 LEU cc_start: 0.9362 (tp) cc_final: 0.9154 (tp) REVERT: A 421 GLU cc_start: 0.8330 (pp20) cc_final: 0.8081 (pp20) REVERT: A 453 ARG cc_start: 0.9181 (ttt-90) cc_final: 0.8930 (ttt180) REVERT: A 475 ASN cc_start: 0.8206 (m110) cc_final: 0.7920 (m-40) REVERT: A 501 GLN cc_start: 0.9272 (tt0) cc_final: 0.8847 (tm-30) REVERT: A 505 GLU cc_start: 0.8587 (pt0) cc_final: 0.8015 (pt0) REVERT: A 509 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8495 (tm-30) REVERT: A 558 TRP cc_start: 0.8955 (m100) cc_final: 0.8553 (m100) REVERT: A 615 MET cc_start: 0.9053 (mmm) cc_final: 0.8617 (mmm) REVERT: A 639 ASP cc_start: 0.8786 (m-30) cc_final: 0.8476 (m-30) REVERT: A 658 LEU cc_start: 0.9625 (mp) cc_final: 0.9381 (mp) REVERT: B 30 LYS cc_start: 0.9140 (tptt) cc_final: 0.8833 (tptp) REVERT: B 40 TYR cc_start: 0.9412 (t80) cc_final: 0.9048 (t80) REVERT: B 99 LYS cc_start: 0.9421 (tptm) cc_final: 0.9067 (tptp) REVERT: B 127 LEU cc_start: 0.9790 (mt) cc_final: 0.9474 (mm) REVERT: B 129 PHE cc_start: 0.9152 (m-80) cc_final: 0.8927 (m-80) REVERT: B 135 GLU cc_start: 0.9011 (mp0) cc_final: 0.8791 (pm20) REVERT: B 147 GLN cc_start: 0.8998 (mt0) cc_final: 0.8536 (mt0) REVERT: B 150 GLN cc_start: 0.9357 (tp-100) cc_final: 0.8806 (tp-100) REVERT: B 184 ARG cc_start: 0.9563 (tpp80) cc_final: 0.9264 (tpp-160) REVERT: B 186 ILE cc_start: 0.9691 (mt) cc_final: 0.9201 (mt) REVERT: B 190 MET cc_start: 0.9288 (mtm) cc_final: 0.8927 (mtm) REVERT: B 216 VAL cc_start: 0.9075 (t) cc_final: 0.8870 (p) REVERT: B 232 ASN cc_start: 0.9115 (m-40) cc_final: 0.8903 (m110) REVERT: B 252 ASN cc_start: 0.9385 (t0) cc_final: 0.8996 (t0) REVERT: B 256 ARG cc_start: 0.8281 (tmt170) cc_final: 0.7951 (ttp80) REVERT: B 257 ASP cc_start: 0.8382 (m-30) cc_final: 0.7633 (m-30) REVERT: B 260 ASP cc_start: 0.9202 (m-30) cc_final: 0.8952 (p0) REVERT: B 286 ASP cc_start: 0.8364 (m-30) cc_final: 0.8047 (m-30) REVERT: B 290 GLU cc_start: 0.9019 (tp30) cc_final: 0.8020 (tp30) REVERT: B 317 MET cc_start: 0.8871 (mtp) cc_final: 0.8560 (mtt) REVERT: B 348 MET cc_start: 0.8936 (ppp) cc_final: 0.8423 (ppp) REVERT: B 349 LEU cc_start: 0.9349 (mt) cc_final: 0.8752 (mt) REVERT: B 361 GLN cc_start: 0.8572 (tt0) cc_final: 0.8307 (tm-30) REVERT: B 375 LYS cc_start: 0.8860 (mmmm) cc_final: 0.8539 (mmmm) REVERT: B 402 GLU cc_start: 0.8151 (mp0) cc_final: 0.7809 (mp0) REVERT: B 415 ASN cc_start: 0.9076 (t0) cc_final: 0.8833 (t0) REVERT: B 437 THR cc_start: 0.9608 (m) cc_final: 0.9303 (m) REVERT: B 493 MET cc_start: 0.9339 (tmm) cc_final: 0.8657 (tmm) REVERT: B 515 ASP cc_start: 0.8892 (m-30) cc_final: 0.8535 (p0) REVERT: B 526 GLU cc_start: 0.8899 (mp0) cc_final: 0.8612 (mp0) REVERT: B 586 TYR cc_start: 0.8980 (m-80) cc_final: 0.8768 (m-80) REVERT: B 612 TYR cc_start: 0.8272 (m-80) cc_final: 0.7799 (m-80) REVERT: B 618 LEU cc_start: 0.8492 (tp) cc_final: 0.8204 (tp) REVERT: B 623 TRP cc_start: 0.8286 (t-100) cc_final: 0.7867 (t-100) REVERT: B 656 LEU cc_start: 0.9323 (mt) cc_final: 0.9092 (mt) REVERT: C 17 PHE cc_start: 0.8901 (p90) cc_final: 0.8134 (p90) REVERT: C 20 MET cc_start: 0.9105 (ppp) cc_final: 0.8817 (ppp) REVERT: C 21 PHE cc_start: 0.8957 (m-80) cc_final: 0.8274 (m-80) REVERT: C 56 MET cc_start: 0.1038 (ptm) cc_final: 0.0542 (ttp) REVERT: C 74 MET cc_start: 0.9386 (mpp) cc_final: 0.9082 (mpp) REVERT: C 89 VAL cc_start: 0.7527 (t) cc_final: 0.6854 (t) REVERT: C 95 MET cc_start: 0.8552 (ttp) cc_final: 0.8095 (ttp) REVERT: C 157 MET cc_start: 0.9409 (mtm) cc_final: 0.9045 (ptt) REVERT: C 163 LEU cc_start: 0.9177 (tt) cc_final: 0.8862 (tp) REVERT: C 174 TYR cc_start: 0.8992 (t80) cc_final: 0.8338 (t80) REVERT: C 212 ILE cc_start: 0.8675 (mt) cc_final: 0.8258 (mm) REVERT: C 226 GLU cc_start: 0.8729 (tt0) cc_final: 0.8470 (tt0) REVERT: C 227 PHE cc_start: 0.8698 (t80) cc_final: 0.8410 (t80) REVERT: C 239 GLU cc_start: 0.9263 (pt0) cc_final: 0.8998 (pt0) REVERT: C 260 ILE cc_start: 0.5966 (pt) cc_final: 0.5548 (pt) REVERT: D 109 PHE cc_start: 0.8688 (m-10) cc_final: 0.8367 (m-80) REVERT: D 115 THR cc_start: 0.8414 (m) cc_final: 0.8211 (p) REVERT: D 128 ASN cc_start: 0.8356 (t0) cc_final: 0.7811 (t0) REVERT: D 133 LYS cc_start: 0.8283 (ttmt) cc_final: 0.8063 (tptp) REVERT: E 25 TRP cc_start: 0.8186 (p-90) cc_final: 0.7544 (p-90) REVERT: E 46 MET cc_start: 0.8147 (tpp) cc_final: 0.7912 (tpp) REVERT: E 70 MET cc_start: 0.8060 (mmp) cc_final: 0.7226 (mpp) outliers start: 1 outliers final: 0 residues processed: 731 average time/residue: 0.2997 time to fit residues: 329.6590 Evaluate side-chains 599 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 599 time to evaluate : 1.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 197 optimal weight: 20.0000 chunk 13 optimal weight: 0.5980 chunk 191 optimal weight: 7.9990 chunk 103 optimal weight: 4.9990 chunk 92 optimal weight: 6.9990 chunk 141 optimal weight: 10.0000 chunk 155 optimal weight: 1.9990 chunk 183 optimal weight: 10.0000 chunk 136 optimal weight: 0.9980 chunk 76 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 270 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 119 ASN D 136 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.132994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096758 restraints weight = 42805.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.100165 restraints weight = 22812.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.102401 restraints weight = 14342.292| |-----------------------------------------------------------------------------| r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3248 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3248 r_free = 0.3248 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3248 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.5891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 17041 Z= 0.188 Angle : 0.623 7.495 23026 Z= 0.326 Chirality : 0.044 0.285 2464 Planarity : 0.004 0.040 2931 Dihedral : 10.346 145.962 2325 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.06 (0.19), residues: 2012 helix: 1.17 (0.15), residues: 1159 sheet: -0.06 (0.40), residues: 165 loop : 0.30 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 623 HIS 0.006 0.001 HIS B 438 PHE 0.034 0.002 PHE C 172 TYR 0.034 0.002 TYR C 169 ARG 0.006 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 912) hydrogen bonds : angle 4.96252 ( 2664) SS BOND : bond 0.00709 ( 3) SS BOND : angle 3.84490 ( 6) covalent geometry : bond 0.00409 (17038) covalent geometry : angle 0.62019 (23020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 706 time to evaluate : 1.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 209 LYS cc_start: 0.9165 (tttm) cc_final: 0.8938 (tttm) REVERT: A 234 PHE cc_start: 0.9525 (m-80) cc_final: 0.9309 (m-80) REVERT: A 256 ARG cc_start: 0.9192 (tmt-80) cc_final: 0.8626 (tmt-80) REVERT: A 320 ASN cc_start: 0.8299 (m110) cc_final: 0.7937 (m110) REVERT: A 322 MET cc_start: 0.8121 (mmm) cc_final: 0.7796 (mmm) REVERT: A 336 LYS cc_start: 0.9031 (tppp) cc_final: 0.8818 (tppt) REVERT: A 345 LYS cc_start: 0.9529 (tttm) cc_final: 0.9224 (tttt) REVERT: A 348 MET cc_start: 0.8938 (ptm) cc_final: 0.8648 (ptm) REVERT: A 362 ASP cc_start: 0.8395 (m-30) cc_final: 0.8086 (m-30) REVERT: A 367 VAL cc_start: 0.9575 (m) cc_final: 0.9309 (p) REVERT: A 390 GLN cc_start: 0.8739 (mt0) cc_final: 0.8439 (mt0) REVERT: A 421 GLU cc_start: 0.8491 (pp20) cc_final: 0.8095 (pp20) REVERT: A 474 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8138 (tm-30) REVERT: A 475 ASN cc_start: 0.8000 (m110) cc_final: 0.7611 (m110) REVERT: A 498 TYR cc_start: 0.8642 (m-80) cc_final: 0.8171 (m-80) REVERT: A 515 ASP cc_start: 0.8901 (m-30) cc_final: 0.8489 (m-30) REVERT: A 615 MET cc_start: 0.9034 (mmm) cc_final: 0.8562 (mmm) REVERT: A 647 HIS cc_start: 0.8922 (m-70) cc_final: 0.8717 (m170) REVERT: A 658 LEU cc_start: 0.9621 (mp) cc_final: 0.9297 (mp) REVERT: B 30 LYS cc_start: 0.9022 (tptt) cc_final: 0.8799 (tptt) REVERT: B 51 LEU cc_start: 0.9298 (tp) cc_final: 0.9093 (tp) REVERT: B 87 LYS cc_start: 0.9124 (tppt) cc_final: 0.8509 (ttmt) REVERT: B 127 LEU cc_start: 0.9805 (mt) cc_final: 0.9531 (mm) REVERT: B 129 PHE cc_start: 0.9168 (m-80) cc_final: 0.8895 (m-80) REVERT: B 145 ILE cc_start: 0.9325 (tp) cc_final: 0.8955 (tp) REVERT: B 147 GLN cc_start: 0.9197 (mt0) cc_final: 0.8310 (mt0) REVERT: B 150 GLN cc_start: 0.9457 (tp40) cc_final: 0.8759 (tp-100) REVERT: B 190 MET cc_start: 0.9243 (mtm) cc_final: 0.9035 (mtm) REVERT: B 205 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7892 (mmmm) REVERT: B 216 VAL cc_start: 0.9016 (t) cc_final: 0.8763 (p) REVERT: B 232 ASN cc_start: 0.9154 (m-40) cc_final: 0.8715 (m110) REVERT: B 256 ARG cc_start: 0.8312 (tmt170) cc_final: 0.7963 (ttp80) REVERT: B 257 ASP cc_start: 0.8257 (m-30) cc_final: 0.7357 (m-30) REVERT: B 260 ASP cc_start: 0.9294 (m-30) cc_final: 0.9018 (p0) REVERT: B 286 ASP cc_start: 0.8354 (m-30) cc_final: 0.8079 (m-30) REVERT: B 290 GLU cc_start: 0.8626 (tp30) cc_final: 0.8318 (tp30) REVERT: B 317 MET cc_start: 0.8818 (mtp) cc_final: 0.8430 (mtt) REVERT: B 335 GLU cc_start: 0.7860 (tm-30) cc_final: 0.7594 (tm-30) REVERT: B 344 GLU cc_start: 0.9169 (pt0) cc_final: 0.8678 (pp20) REVERT: B 348 MET cc_start: 0.8995 (ppp) cc_final: 0.8523 (ppp) REVERT: B 349 LEU cc_start: 0.9357 (mt) cc_final: 0.8662 (mt) REVERT: B 361 GLN cc_start: 0.8585 (tt0) cc_final: 0.8246 (tp40) REVERT: B 402 GLU cc_start: 0.8137 (mp0) cc_final: 0.7415 (mp0) REVERT: B 415 ASN cc_start: 0.9112 (t0) cc_final: 0.8860 (t0) REVERT: B 416 ILE cc_start: 0.8748 (mm) cc_final: 0.8531 (mm) REVERT: B 437 THR cc_start: 0.9595 (m) cc_final: 0.9230 (m) REVERT: B 446 ARG cc_start: 0.7399 (mmt-90) cc_final: 0.7159 (mmt-90) REVERT: B 475 ASN cc_start: 0.8766 (m-40) cc_final: 0.8528 (m110) REVERT: B 493 MET cc_start: 0.9344 (tmm) cc_final: 0.8699 (tmm) REVERT: B 515 ASP cc_start: 0.8963 (m-30) cc_final: 0.8577 (p0) REVERT: B 526 GLU cc_start: 0.8834 (mp0) cc_final: 0.8515 (mp0) REVERT: B 612 TYR cc_start: 0.8160 (m-80) cc_final: 0.7755 (m-80) REVERT: B 618 LEU cc_start: 0.8576 (tp) cc_final: 0.8292 (tp) REVERT: B 623 TRP cc_start: 0.8375 (t-100) cc_final: 0.7699 (t-100) REVERT: B 656 LEU cc_start: 0.9315 (mt) cc_final: 0.9104 (mt) REVERT: C 17 PHE cc_start: 0.8987 (p90) cc_final: 0.8310 (p90) REVERT: C 20 MET cc_start: 0.9170 (ppp) cc_final: 0.8864 (ppp) REVERT: C 21 PHE cc_start: 0.9028 (m-80) cc_final: 0.8426 (m-80) REVERT: C 56 MET cc_start: 0.1308 (ptm) cc_final: 0.0678 (ttp) REVERT: C 69 GLN cc_start: 0.8981 (tp40) cc_final: 0.8652 (tp-100) REVERT: C 95 MET cc_start: 0.8642 (ttp) cc_final: 0.8053 (ttp) REVERT: C 154 PHE cc_start: 0.9131 (t80) cc_final: 0.8823 (t80) REVERT: C 157 MET cc_start: 0.9424 (mtm) cc_final: 0.9086 (ptt) REVERT: C 163 LEU cc_start: 0.9262 (tt) cc_final: 0.8945 (tp) REVERT: C 174 TYR cc_start: 0.8993 (t80) cc_final: 0.8227 (t80) REVERT: C 187 SER cc_start: 0.8209 (m) cc_final: 0.7960 (p) REVERT: C 212 ILE cc_start: 0.8776 (mt) cc_final: 0.8372 (mm) REVERT: C 226 GLU cc_start: 0.8733 (tt0) cc_final: 0.8518 (tt0) REVERT: C 230 ASP cc_start: 0.9136 (m-30) cc_final: 0.8930 (m-30) REVERT: C 231 LEU cc_start: 0.9091 (mt) cc_final: 0.8783 (mt) REVERT: C 239 GLU cc_start: 0.9167 (pt0) cc_final: 0.8847 (pt0) REVERT: D 35 ILE cc_start: 0.7193 (mm) cc_final: 0.6926 (mm) REVERT: D 109 PHE cc_start: 0.8675 (m-10) cc_final: 0.8251 (m-80) REVERT: D 128 ASN cc_start: 0.8268 (t0) cc_final: 0.7180 (t0) REVERT: D 133 LYS cc_start: 0.8513 (ttmt) cc_final: 0.8113 (tptp) REVERT: D 242 TYR cc_start: 0.7853 (t80) cc_final: 0.7318 (t80) REVERT: E 25 TRP cc_start: 0.8261 (p-90) cc_final: 0.7894 (p-90) REVERT: E 46 MET cc_start: 0.8306 (tpp) cc_final: 0.8057 (tpp) REVERT: E 60 ASN cc_start: 0.9435 (t0) cc_final: 0.9209 (t0) outliers start: 0 outliers final: 0 residues processed: 706 average time/residue: 0.2877 time to fit residues: 302.7237 Evaluate side-chains 583 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 583 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.8980 chunk 124 optimal weight: 3.9990 chunk 109 optimal weight: 0.9990 chunk 144 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 118 optimal weight: 0.8980 chunk 123 optimal weight: 0.6980 chunk 128 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 9.9990 chunk 15 optimal weight: 4.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN A 180 ASN A 304 HIS ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 501 GLN ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 218 ASN B 312 GLN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3803 r_free = 0.3803 target = 0.135532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.097537 restraints weight = 42099.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.101220 restraints weight = 21800.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.103572 restraints weight = 13532.723| |-----------------------------------------------------------------------------| r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3290 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3290 r_free = 0.3290 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3290 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7480 moved from start: 0.6243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 17041 Z= 0.138 Angle : 0.613 8.668 23026 Z= 0.319 Chirality : 0.044 0.327 2464 Planarity : 0.004 0.053 2931 Dihedral : 10.226 143.045 2325 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 0.17 % Allowed : 1.73 % Favored : 98.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 1.02 (0.19), residues: 2012 helix: 1.17 (0.15), residues: 1155 sheet: -0.14 (0.41), residues: 171 loop : 0.26 (0.24), residues: 686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 PHE 0.032 0.002 PHE B 81 TYR 0.025 0.001 TYR D 105 ARG 0.007 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03882 ( 912) hydrogen bonds : angle 4.89595 ( 2664) SS BOND : bond 0.00864 ( 3) SS BOND : angle 4.46000 ( 6) covalent geometry : bond 0.00309 (17038) covalent geometry : angle 0.60848 (23020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 703 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 700 time to evaluate : 1.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 GLU cc_start: 0.8567 (tp30) cc_final: 0.8322 (tp30) REVERT: A 187 ASP cc_start: 0.8684 (t70) cc_final: 0.8250 (t0) REVERT: A 209 LYS cc_start: 0.9141 (tttm) cc_final: 0.8784 (tttm) REVERT: A 223 VAL cc_start: 0.9195 (p) cc_final: 0.8916 (p) REVERT: A 234 PHE cc_start: 0.9464 (m-80) cc_final: 0.9257 (m-80) REVERT: A 250 TYR cc_start: 0.8094 (m-80) cc_final: 0.7620 (m-80) REVERT: A 254 PHE cc_start: 0.8829 (m-80) cc_final: 0.8342 (m-80) REVERT: A 256 ARG cc_start: 0.9207 (tmt-80) cc_final: 0.8974 (ttp80) REVERT: A 257 ASP cc_start: 0.8671 (m-30) cc_final: 0.7856 (m-30) REVERT: A 286 ASP cc_start: 0.8852 (m-30) cc_final: 0.8533 (m-30) REVERT: A 290 GLU cc_start: 0.9137 (tm-30) cc_final: 0.8852 (tm-30) REVERT: A 312 GLN cc_start: 0.8346 (tp-100) cc_final: 0.8076 (tp40) REVERT: A 336 LYS cc_start: 0.8951 (tppp) cc_final: 0.8746 (tppt) REVERT: A 338 ASN cc_start: 0.9482 (t0) cc_final: 0.9154 (t0) REVERT: A 367 VAL cc_start: 0.9552 (m) cc_final: 0.9307 (p) REVERT: A 390 GLN cc_start: 0.8730 (mt0) cc_final: 0.8494 (mt0) REVERT: A 421 GLU cc_start: 0.8518 (pp20) cc_final: 0.8120 (pp20) REVERT: A 491 PHE cc_start: 0.9532 (t80) cc_final: 0.9253 (t80) REVERT: A 498 TYR cc_start: 0.8660 (m-80) cc_final: 0.8169 (m-80) REVERT: A 501 GLN cc_start: 0.9319 (OUTLIER) cc_final: 0.8484 (tm-30) REVERT: A 505 GLU cc_start: 0.8672 (pt0) cc_final: 0.8172 (pt0) REVERT: A 515 ASP cc_start: 0.8891 (m-30) cc_final: 0.8500 (m-30) REVERT: A 615 MET cc_start: 0.9026 (mmm) cc_final: 0.8517 (mmm) REVERT: A 645 GLN cc_start: 0.8637 (tp40) cc_final: 0.7826 (tp40) REVERT: A 646 GLN cc_start: 0.8528 (pt0) cc_final: 0.8174 (pt0) REVERT: A 647 HIS cc_start: 0.8670 (m-70) cc_final: 0.7933 (m90) REVERT: A 686 ARG cc_start: 0.8117 (ttm-80) cc_final: 0.7855 (mtp85) REVERT: B 23 LYS cc_start: 0.9266 (mmpt) cc_final: 0.8998 (mmmt) REVERT: B 30 LYS cc_start: 0.8993 (tptt) cc_final: 0.8782 (tptt) REVERT: B 52 LYS cc_start: 0.9416 (tptt) cc_final: 0.9004 (tppt) REVERT: B 56 ASP cc_start: 0.9298 (m-30) cc_final: 0.8978 (m-30) REVERT: B 87 LYS cc_start: 0.9098 (tppt) cc_final: 0.8485 (ttmt) REVERT: B 99 LYS cc_start: 0.9442 (tptm) cc_final: 0.9234 (tptm) REVERT: B 117 ARG cc_start: 0.8140 (mmm160) cc_final: 0.7740 (mmm-85) REVERT: B 120 ASP cc_start: 0.8830 (m-30) cc_final: 0.8364 (m-30) REVERT: B 127 LEU cc_start: 0.9777 (mt) cc_final: 0.9488 (mm) REVERT: B 129 PHE cc_start: 0.9157 (m-10) cc_final: 0.8817 (m-80) REVERT: B 145 ILE cc_start: 0.9333 (tp) cc_final: 0.8986 (tp) REVERT: B 147 GLN cc_start: 0.9097 (mt0) cc_final: 0.8129 (mt0) REVERT: B 184 ARG cc_start: 0.9563 (tpp80) cc_final: 0.9061 (tpp80) REVERT: B 216 VAL cc_start: 0.9030 (t) cc_final: 0.8766 (p) REVERT: B 227 MET cc_start: 0.9199 (mtp) cc_final: 0.8992 (mtp) REVERT: B 231 ASP cc_start: 0.8437 (t70) cc_final: 0.7483 (t70) REVERT: B 232 ASN cc_start: 0.9045 (m-40) cc_final: 0.8705 (m110) REVERT: B 235 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.7865 (mtm-85) REVERT: B 256 ARG cc_start: 0.8323 (tmt170) cc_final: 0.8047 (ttp80) REVERT: B 257 ASP cc_start: 0.8102 (m-30) cc_final: 0.7506 (m-30) REVERT: B 260 ASP cc_start: 0.9247 (m-30) cc_final: 0.8972 (p0) REVERT: B 286 ASP cc_start: 0.8362 (m-30) cc_final: 0.8108 (m-30) REVERT: B 290 GLU cc_start: 0.8667 (tp30) cc_final: 0.7965 (tp30) REVERT: B 294 GLU cc_start: 0.8458 (mp0) cc_final: 0.7845 (mp0) REVERT: B 344 GLU cc_start: 0.9174 (pt0) cc_final: 0.8658 (pp20) REVERT: B 348 MET cc_start: 0.9018 (ppp) cc_final: 0.8519 (ppp) REVERT: B 349 LEU cc_start: 0.9365 (mt) cc_final: 0.8655 (mt) REVERT: B 375 LYS cc_start: 0.9037 (mmmm) cc_final: 0.8459 (mmmm) REVERT: B 402 GLU cc_start: 0.8143 (mp0) cc_final: 0.7475 (mp0) REVERT: B 426 GLU cc_start: 0.8767 (tp30) cc_final: 0.8223 (tp30) REVERT: B 427 LYS cc_start: 0.9139 (ptpp) cc_final: 0.8911 (ptpp) REVERT: B 437 THR cc_start: 0.9536 (m) cc_final: 0.9219 (m) REVERT: B 446 ARG cc_start: 0.7389 (mmt-90) cc_final: 0.7187 (mmt-90) REVERT: B 475 ASN cc_start: 0.9158 (m-40) cc_final: 0.8803 (m110) REVERT: B 493 MET cc_start: 0.9252 (tmm) cc_final: 0.8534 (tmm) REVERT: B 526 GLU cc_start: 0.8902 (mp0) cc_final: 0.8622 (mp0) REVERT: B 602 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8413 (mt-10) REVERT: B 612 TYR cc_start: 0.8077 (m-80) cc_final: 0.7726 (m-80) REVERT: B 656 LEU cc_start: 0.9332 (mt) cc_final: 0.9012 (mt) REVERT: C 17 PHE cc_start: 0.8945 (p90) cc_final: 0.8241 (p90) REVERT: C 20 MET cc_start: 0.9276 (ppp) cc_final: 0.8997 (ppp) REVERT: C 21 PHE cc_start: 0.8992 (m-80) cc_final: 0.8395 (m-80) REVERT: C 46 TYR cc_start: 0.8372 (m-80) cc_final: 0.7786 (m-80) REVERT: C 56 MET cc_start: 0.1146 (ptm) cc_final: 0.0577 (ttp) REVERT: C 74 MET cc_start: 0.9342 (mpp) cc_final: 0.9019 (mpp) REVERT: C 89 VAL cc_start: 0.6963 (m) cc_final: 0.6286 (m) REVERT: C 95 MET cc_start: 0.8555 (ttp) cc_final: 0.8118 (ttp) REVERT: C 163 LEU cc_start: 0.9246 (tt) cc_final: 0.8937 (tt) REVERT: C 174 TYR cc_start: 0.8942 (t80) cc_final: 0.8162 (t80) REVERT: C 231 LEU cc_start: 0.8990 (mt) cc_final: 0.8773 (mt) REVERT: C 274 ASP cc_start: 0.8844 (p0) cc_final: 0.8585 (p0) REVERT: D 45 LYS cc_start: 0.9060 (pttp) cc_final: 0.8779 (pttm) REVERT: D 128 ASN cc_start: 0.8352 (t0) cc_final: 0.7825 (t0) REVERT: E 25 TRP cc_start: 0.8126 (p-90) cc_final: 0.7509 (p-90) REVERT: E 46 MET cc_start: 0.8313 (tpp) cc_final: 0.8035 (tpp) REVERT: E 60 ASN cc_start: 0.9410 (t0) cc_final: 0.9153 (t0) outliers start: 3 outliers final: 0 residues processed: 700 average time/residue: 0.2800 time to fit residues: 292.8974 Evaluate side-chains 567 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 566 time to evaluate : 1.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 0.7980 chunk 119 optimal weight: 4.9990 chunk 170 optimal weight: 3.9990 chunk 186 optimal weight: 10.0000 chunk 30 optimal weight: 0.5980 chunk 5 optimal weight: 7.9990 chunk 193 optimal weight: 7.9990 chunk 17 optimal weight: 8.9990 chunk 77 optimal weight: 8.9990 chunk 135 optimal weight: 8.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 218 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.131318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.095602 restraints weight = 43571.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.098874 restraints weight = 23125.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100988 restraints weight = 14612.888| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3251 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3251 r_free = 0.3251 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3250 r_free = 0.3250 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3250 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.6555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 17041 Z= 0.205 Angle : 0.653 9.723 23026 Z= 0.341 Chirality : 0.044 0.281 2464 Planarity : 0.004 0.058 2931 Dihedral : 10.248 146.666 2325 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.06 % Allowed : 1.68 % Favored : 98.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.87 (0.19), residues: 2012 helix: 1.06 (0.15), residues: 1147 sheet: -0.25 (0.39), residues: 163 loop : 0.17 (0.24), residues: 702 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 623 HIS 0.006 0.001 HIS B 255 PHE 0.041 0.002 PHE D 122 TYR 0.030 0.002 TYR D 105 ARG 0.006 0.001 ARG A 446 Details of bonding type rmsd hydrogen bonds : bond 0.03959 ( 912) hydrogen bonds : angle 4.98217 ( 2664) SS BOND : bond 0.00842 ( 3) SS BOND : angle 4.17050 ( 6) covalent geometry : bond 0.00450 (17038) covalent geometry : angle 0.64962 (23020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 670 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 669 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9081 (tptp) cc_final: 0.8604 (tppt) REVERT: A 12 LEU cc_start: 0.9604 (mt) cc_final: 0.9331 (mt) REVERT: A 66 GLU cc_start: 0.8540 (tp30) cc_final: 0.8303 (tp30) REVERT: A 117 ARG cc_start: 0.8522 (mmt180) cc_final: 0.8313 (mtt-85) REVERT: A 157 LEU cc_start: 0.9298 (tp) cc_final: 0.8997 (tp) REVERT: A 250 TYR cc_start: 0.8068 (m-80) cc_final: 0.7727 (m-80) REVERT: A 254 PHE cc_start: 0.8901 (m-80) cc_final: 0.8403 (m-80) REVERT: A 256 ARG cc_start: 0.9280 (tmt-80) cc_final: 0.8657 (tmt-80) REVERT: A 262 LEU cc_start: 0.9253 (pp) cc_final: 0.9052 (pp) REVERT: A 290 GLU cc_start: 0.9159 (tm-30) cc_final: 0.8757 (tm-30) REVERT: A 291 LEU cc_start: 0.9530 (mm) cc_final: 0.9231 (mm) REVERT: A 338 ASN cc_start: 0.9355 (t0) cc_final: 0.8203 (t0) REVERT: A 341 LYS cc_start: 0.9668 (mttt) cc_final: 0.9462 (mttt) REVERT: A 367 VAL cc_start: 0.9606 (m) cc_final: 0.9363 (p) REVERT: A 390 GLN cc_start: 0.8884 (mt0) cc_final: 0.8620 (mt0) REVERT: A 421 GLU cc_start: 0.8544 (pp20) cc_final: 0.8181 (pp20) REVERT: A 468 LEU cc_start: 0.9371 (tp) cc_final: 0.9169 (tp) REVERT: A 490 THR cc_start: 0.8512 (p) cc_final: 0.7287 (t) REVERT: A 491 PHE cc_start: 0.9643 (t80) cc_final: 0.9250 (t80) REVERT: A 498 TYR cc_start: 0.8750 (m-80) cc_final: 0.8318 (m-80) REVERT: A 501 GLN cc_start: 0.9309 (tt0) cc_final: 0.8188 (tm-30) REVERT: A 505 GLU cc_start: 0.8651 (pt0) cc_final: 0.8262 (pt0) REVERT: A 510 LYS cc_start: 0.9219 (mttt) cc_final: 0.9015 (mtmt) REVERT: A 515 ASP cc_start: 0.8946 (m-30) cc_final: 0.8577 (m-30) REVERT: A 571 TYR cc_start: 0.8215 (t80) cc_final: 0.7860 (t80) REVERT: A 615 MET cc_start: 0.8959 (mmm) cc_final: 0.8461 (mmm) REVERT: A 646 GLN cc_start: 0.8647 (pt0) cc_final: 0.8315 (pt0) REVERT: A 647 HIS cc_start: 0.8837 (m-70) cc_final: 0.8181 (m90) REVERT: A 655 THR cc_start: 0.9061 (m) cc_final: 0.8860 (m) REVERT: A 668 ASN cc_start: 0.9192 (m-40) cc_final: 0.8859 (p0) REVERT: A 686 ARG cc_start: 0.8232 (ttm-80) cc_final: 0.7937 (mtp180) REVERT: B 16 ILE cc_start: 0.9316 (tp) cc_final: 0.9002 (tp) REVERT: B 18 ILE cc_start: 0.9398 (mm) cc_final: 0.8629 (mm) REVERT: B 27 ASP cc_start: 0.9435 (p0) cc_final: 0.9075 (p0) REVERT: B 51 LEU cc_start: 0.9480 (tp) cc_final: 0.9181 (tp) REVERT: B 87 LYS cc_start: 0.9175 (tppt) cc_final: 0.8548 (ttmt) REVERT: B 99 LYS cc_start: 0.9432 (tptm) cc_final: 0.9214 (tptm) REVERT: B 112 LYS cc_start: 0.9453 (mmpt) cc_final: 0.9246 (mmmt) REVERT: B 117 ARG cc_start: 0.8190 (mmm160) cc_final: 0.7634 (mmm-85) REVERT: B 120 ASP cc_start: 0.8751 (m-30) cc_final: 0.8351 (m-30) REVERT: B 127 LEU cc_start: 0.9788 (mt) cc_final: 0.9500 (mm) REVERT: B 129 PHE cc_start: 0.9153 (m-10) cc_final: 0.8870 (m-80) REVERT: B 145 ILE cc_start: 0.9364 (tp) cc_final: 0.8936 (tp) REVERT: B 147 GLN cc_start: 0.9236 (mt0) cc_final: 0.8761 (mt0) REVERT: B 184 ARG cc_start: 0.9535 (tpp80) cc_final: 0.9055 (tpp80) REVERT: B 186 ILE cc_start: 0.9540 (mt) cc_final: 0.9299 (mt) REVERT: B 190 MET cc_start: 0.9363 (mtm) cc_final: 0.8828 (mtm) REVERT: B 216 VAL cc_start: 0.9018 (t) cc_final: 0.8748 (p) REVERT: B 231 ASP cc_start: 0.8453 (t70) cc_final: 0.7275 (t70) REVERT: B 232 ASN cc_start: 0.9152 (m-40) cc_final: 0.8782 (m110) REVERT: B 235 ARG cc_start: 0.8763 (mtm-85) cc_final: 0.7782 (mtm-85) REVERT: B 256 ARG cc_start: 0.8290 (tmt170) cc_final: 0.8050 (ttp80) REVERT: B 257 ASP cc_start: 0.8367 (m-30) cc_final: 0.7415 (m-30) REVERT: B 260 ASP cc_start: 0.9300 (m-30) cc_final: 0.9027 (p0) REVERT: B 335 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7774 (tm-30) REVERT: B 343 LEU cc_start: 0.9760 (mt) cc_final: 0.9509 (mm) REVERT: B 344 GLU cc_start: 0.9197 (pt0) cc_final: 0.8687 (pp20) REVERT: B 348 MET cc_start: 0.9026 (ppp) cc_final: 0.8455 (ppp) REVERT: B 349 LEU cc_start: 0.9393 (mt) cc_final: 0.8746 (mt) REVERT: B 358 ILE cc_start: 0.9610 (mm) cc_final: 0.9284 (mm) REVERT: B 361 GLN cc_start: 0.8540 (tt0) cc_final: 0.8331 (tp40) REVERT: B 378 PHE cc_start: 0.8844 (p90) cc_final: 0.8427 (p90) REVERT: B 402 GLU cc_start: 0.8215 (mp0) cc_final: 0.7509 (mp0) REVERT: B 437 THR cc_start: 0.9572 (m) cc_final: 0.9180 (m) REVERT: B 475 ASN cc_start: 0.9100 (m-40) cc_final: 0.8772 (m110) REVERT: B 526 GLU cc_start: 0.8951 (mp0) cc_final: 0.8675 (mp0) REVERT: B 570 MET cc_start: 0.8566 (tpp) cc_final: 0.6668 (tpp) REVERT: B 599 GLU cc_start: 0.9091 (pm20) cc_final: 0.8725 (pm20) REVERT: B 612 TYR cc_start: 0.8390 (m-80) cc_final: 0.8006 (m-80) REVERT: B 624 PHE cc_start: 0.8663 (m-80) cc_final: 0.8391 (m-80) REVERT: B 656 LEU cc_start: 0.9284 (mt) cc_final: 0.9010 (mt) REVERT: C 17 PHE cc_start: 0.9024 (p90) cc_final: 0.8345 (p90) REVERT: C 20 MET cc_start: 0.9281 (ppp) cc_final: 0.9011 (ppp) REVERT: C 21 PHE cc_start: 0.8995 (m-80) cc_final: 0.8444 (m-80) REVERT: C 46 TYR cc_start: 0.8080 (m-80) cc_final: 0.7789 (m-80) REVERT: C 56 MET cc_start: 0.1148 (ptm) cc_final: 0.0530 (ttp) REVERT: C 68 GLU cc_start: 0.8946 (mp0) cc_final: 0.8730 (pm20) REVERT: C 74 MET cc_start: 0.9263 (mpp) cc_final: 0.8998 (mpp) REVERT: C 89 VAL cc_start: 0.7124 (m) cc_final: 0.6746 (t) REVERT: C 95 MET cc_start: 0.8490 (ttp) cc_final: 0.7924 (ttp) REVERT: C 157 MET cc_start: 0.9380 (mtm) cc_final: 0.8772 (ptp) REVERT: C 174 TYR cc_start: 0.8870 (t80) cc_final: 0.7979 (t80) REVERT: C 226 GLU cc_start: 0.8945 (tt0) cc_final: 0.8739 (tt0) REVERT: C 231 LEU cc_start: 0.8973 (mt) cc_final: 0.8768 (mt) REVERT: C 274 ASP cc_start: 0.8960 (p0) cc_final: 0.8716 (p0) REVERT: C 315 LEU cc_start: 0.8263 (mt) cc_final: 0.7403 (mt) REVERT: D 92 PHE cc_start: 0.7151 (t80) cc_final: 0.6879 (t80) REVERT: D 96 MET cc_start: 0.7831 (tpt) cc_final: 0.7515 (tpt) REVERT: E 24 PHE cc_start: 0.8843 (m-80) cc_final: 0.8623 (m-80) REVERT: E 25 TRP cc_start: 0.8105 (p-90) cc_final: 0.7487 (p-90) REVERT: E 46 MET cc_start: 0.8309 (tpp) cc_final: 0.8035 (tpp) REVERT: E 60 ASN cc_start: 0.9404 (t0) cc_final: 0.9146 (t0) outliers start: 1 outliers final: 0 residues processed: 669 average time/residue: 0.2788 time to fit residues: 279.4642 Evaluate side-chains 547 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 2.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 149 optimal weight: 9.9990 chunk 20 optimal weight: 4.9990 chunk 137 optimal weight: 5.9990 chunk 141 optimal weight: 7.9990 chunk 65 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 97 optimal weight: 0.6980 chunk 132 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 25 GLN B 218 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.137196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.100304 restraints weight = 42887.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.103838 restraints weight = 22565.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.106076 restraints weight = 14071.285| |-----------------------------------------------------------------------------| r_work (final): 0.3297 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3296 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3296 r_free = 0.3296 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3296 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.6806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 17041 Z= 0.138 Angle : 0.628 8.524 23026 Z= 0.327 Chirality : 0.044 0.232 2464 Planarity : 0.004 0.043 2931 Dihedral : 10.059 143.098 2325 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.93 (0.18), residues: 2012 helix: 1.07 (0.15), residues: 1136 sheet: 0.61 (0.46), residues: 125 loop : 0.09 (0.22), residues: 751 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 124 HIS 0.006 0.001 HIS B 438 PHE 0.031 0.002 PHE D 122 TYR 0.025 0.002 TYR D 105 ARG 0.005 0.001 ARG D 225 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 912) hydrogen bonds : angle 4.94727 ( 2664) SS BOND : bond 0.00741 ( 3) SS BOND : angle 4.08525 ( 6) covalent geometry : bond 0.00309 (17038) covalent geometry : angle 0.62436 (23020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 667 time to evaluate : 1.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9094 (tptp) cc_final: 0.8619 (tppt) REVERT: A 12 LEU cc_start: 0.9583 (mt) cc_final: 0.9267 (mt) REVERT: A 66 GLU cc_start: 0.8487 (tp30) cc_final: 0.8229 (tp30) REVERT: A 87 LYS cc_start: 0.8709 (tttp) cc_final: 0.8474 (ttmm) REVERT: A 117 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8162 (mtt-85) REVERT: A 184 ARG cc_start: 0.9361 (mmm-85) cc_final: 0.9142 (mmm-85) REVERT: A 209 LYS cc_start: 0.9222 (tttm) cc_final: 0.8952 (tttm) REVERT: A 230 LEU cc_start: 0.9727 (mt) cc_final: 0.9527 (mt) REVERT: A 250 TYR cc_start: 0.8163 (m-80) cc_final: 0.7907 (m-80) REVERT: A 254 PHE cc_start: 0.8833 (m-80) cc_final: 0.8299 (m-80) REVERT: A 256 ARG cc_start: 0.9259 (tmt-80) cc_final: 0.9026 (ttp80) REVERT: A 257 ASP cc_start: 0.8741 (m-30) cc_final: 0.7831 (m-30) REVERT: A 262 LEU cc_start: 0.9287 (pp) cc_final: 0.9085 (pp) REVERT: A 290 GLU cc_start: 0.9111 (tm-30) cc_final: 0.8620 (tm-30) REVERT: A 291 LEU cc_start: 0.9516 (mm) cc_final: 0.9044 (mm) REVERT: A 316 GLU cc_start: 0.7773 (pm20) cc_final: 0.7438 (pm20) REVERT: A 338 ASN cc_start: 0.9271 (t0) cc_final: 0.8146 (t0) REVERT: A 341 LYS cc_start: 0.9660 (mttt) cc_final: 0.9460 (mttt) REVERT: A 362 ASP cc_start: 0.8059 (m-30) cc_final: 0.7668 (m-30) REVERT: A 367 VAL cc_start: 0.9591 (m) cc_final: 0.9364 (p) REVERT: A 390 GLN cc_start: 0.8886 (mt0) cc_final: 0.8608 (mt0) REVERT: A 421 GLU cc_start: 0.8585 (pp20) cc_final: 0.8168 (pp20) REVERT: A 490 THR cc_start: 0.8505 (p) cc_final: 0.7330 (t) REVERT: A 491 PHE cc_start: 0.9603 (t80) cc_final: 0.9395 (t80) REVERT: A 493 MET cc_start: 0.7934 (tmm) cc_final: 0.7515 (tmm) REVERT: A 501 GLN cc_start: 0.9235 (tt0) cc_final: 0.8152 (tm-30) REVERT: A 505 GLU cc_start: 0.8680 (pt0) cc_final: 0.8176 (pt0) REVERT: A 515 ASP cc_start: 0.8885 (m-30) cc_final: 0.8459 (m-30) REVERT: A 590 SER cc_start: 0.9605 (t) cc_final: 0.9144 (p) REVERT: A 615 MET cc_start: 0.8949 (mmm) cc_final: 0.8479 (mmm) REVERT: A 646 GLN cc_start: 0.8670 (pt0) cc_final: 0.8340 (pt0) REVERT: A 647 HIS cc_start: 0.8558 (m-70) cc_final: 0.7915 (m90) REVERT: A 655 THR cc_start: 0.9088 (m) cc_final: 0.8459 (t) REVERT: A 668 ASN cc_start: 0.9130 (m-40) cc_final: 0.8851 (p0) REVERT: A 686 ARG cc_start: 0.8298 (ttm-80) cc_final: 0.8037 (mtp180) REVERT: B 30 LYS cc_start: 0.9267 (tmtt) cc_final: 0.9050 (tptt) REVERT: B 66 GLU cc_start: 0.8392 (tp30) cc_final: 0.8142 (tp30) REVERT: B 87 LYS cc_start: 0.9122 (tppt) cc_final: 0.8517 (ttmt) REVERT: B 112 LYS cc_start: 0.9424 (mmpt) cc_final: 0.9219 (mmmt) REVERT: B 120 ASP cc_start: 0.8693 (m-30) cc_final: 0.8491 (m-30) REVERT: B 127 LEU cc_start: 0.9764 (mt) cc_final: 0.9466 (mm) REVERT: B 129 PHE cc_start: 0.9181 (m-10) cc_final: 0.8869 (m-80) REVERT: B 145 ILE cc_start: 0.9323 (tp) cc_final: 0.8941 (tp) REVERT: B 147 GLN cc_start: 0.9166 (mt0) cc_final: 0.8229 (mt0) REVERT: B 184 ARG cc_start: 0.9557 (tpp80) cc_final: 0.9240 (tpp80) REVERT: B 186 ILE cc_start: 0.9569 (mt) cc_final: 0.9304 (mt) REVERT: B 190 MET cc_start: 0.9323 (mtm) cc_final: 0.8995 (mtm) REVERT: B 216 VAL cc_start: 0.8986 (t) cc_final: 0.8725 (p) REVERT: B 231 ASP cc_start: 0.8418 (t70) cc_final: 0.7184 (t70) REVERT: B 232 ASN cc_start: 0.9023 (m-40) cc_final: 0.8588 (m110) REVERT: B 235 ARG cc_start: 0.8820 (mtm-85) cc_final: 0.7847 (mtm-85) REVERT: B 239 GLN cc_start: 0.7438 (mt0) cc_final: 0.6993 (tm-30) REVERT: B 256 ARG cc_start: 0.8179 (tmt170) cc_final: 0.7956 (ttp80) REVERT: B 257 ASP cc_start: 0.8344 (m-30) cc_final: 0.7364 (m-30) REVERT: B 260 ASP cc_start: 0.9278 (m-30) cc_final: 0.9019 (p0) REVERT: B 286 ASP cc_start: 0.8495 (m-30) cc_final: 0.8086 (m-30) REVERT: B 348 MET cc_start: 0.9062 (ppp) cc_final: 0.8580 (ppp) REVERT: B 349 LEU cc_start: 0.9338 (mt) cc_final: 0.8625 (mt) REVERT: B 358 ILE cc_start: 0.9577 (mm) cc_final: 0.9316 (mm) REVERT: B 378 PHE cc_start: 0.8786 (p90) cc_final: 0.8556 (p90) REVERT: B 394 TYR cc_start: 0.8817 (m-80) cc_final: 0.8555 (m-80) REVERT: B 402 GLU cc_start: 0.8248 (mp0) cc_final: 0.7569 (mp0) REVERT: B 437 THR cc_start: 0.9499 (m) cc_final: 0.9168 (m) REVERT: B 475 ASN cc_start: 0.8973 (m-40) cc_final: 0.8663 (m110) REVERT: B 515 ASP cc_start: 0.8972 (m-30) cc_final: 0.8507 (p0) REVERT: B 570 MET cc_start: 0.8547 (tpp) cc_final: 0.6653 (tpp) REVERT: B 599 GLU cc_start: 0.9003 (pm20) cc_final: 0.8764 (pm20) REVERT: B 602 GLU cc_start: 0.8780 (mt-10) cc_final: 0.8578 (mt-10) REVERT: B 656 LEU cc_start: 0.9269 (mt) cc_final: 0.8980 (mt) REVERT: C 17 PHE cc_start: 0.8983 (p90) cc_final: 0.8296 (p90) REVERT: C 20 MET cc_start: 0.9389 (ppp) cc_final: 0.9160 (ppp) REVERT: C 21 PHE cc_start: 0.9027 (m-80) cc_final: 0.8496 (m-80) REVERT: C 46 TYR cc_start: 0.8137 (m-80) cc_final: 0.7716 (m-80) REVERT: C 56 MET cc_start: 0.1039 (ptm) cc_final: 0.0435 (ttp) REVERT: C 74 MET cc_start: 0.9249 (mpp) cc_final: 0.9014 (mpp) REVERT: C 95 MET cc_start: 0.8578 (ttp) cc_final: 0.7881 (ttp) REVERT: C 129 LYS cc_start: 0.9251 (tptp) cc_final: 0.8916 (tmtt) REVERT: C 163 LEU cc_start: 0.9249 (tt) cc_final: 0.9006 (tt) REVERT: C 174 TYR cc_start: 0.8779 (t80) cc_final: 0.8127 (t80) REVERT: C 231 LEU cc_start: 0.8982 (mt) cc_final: 0.8777 (mt) REVERT: C 274 ASP cc_start: 0.9011 (p0) cc_final: 0.8672 (p0) REVERT: C 315 LEU cc_start: 0.8272 (mt) cc_final: 0.7264 (mt) REVERT: D 25 ASN cc_start: 0.9458 (m-40) cc_final: 0.9242 (m-40) REVERT: D 92 PHE cc_start: 0.7102 (t80) cc_final: 0.6868 (t80) REVERT: D 128 ASN cc_start: 0.8364 (t0) cc_final: 0.7556 (t0) REVERT: D 242 TYR cc_start: 0.7857 (t80) cc_final: 0.7432 (t80) REVERT: E 25 TRP cc_start: 0.8063 (p-90) cc_final: 0.7403 (p-90) REVERT: E 60 ASN cc_start: 0.9384 (t0) cc_final: 0.9104 (t0) outliers start: 1 outliers final: 0 residues processed: 667 average time/residue: 0.2817 time to fit residues: 283.0805 Evaluate side-chains 547 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 547 time to evaluate : 1.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 104 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 chunk 139 optimal weight: 6.9990 chunk 44 optimal weight: 0.3980 chunk 30 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 194 optimal weight: 9.9990 chunk 67 optimal weight: 5.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 150 GLN B 218 ASN ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3753 r_free = 0.3753 target = 0.127084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.090940 restraints weight = 43420.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.094138 restraints weight = 23496.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.096302 restraints weight = 15027.286| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3235 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3235 r_free = 0.3235 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3235 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.7037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 17041 Z= 0.224 Angle : 0.690 11.393 23026 Z= 0.359 Chirality : 0.046 0.317 2464 Planarity : 0.004 0.046 2931 Dihedral : 10.120 148.143 2325 Min Nonbonded Distance : 1.779 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.06 % Allowed : 1.45 % Favored : 98.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.74 (0.18), residues: 2012 helix: 1.01 (0.15), residues: 1141 sheet: -0.36 (0.39), residues: 163 loop : 0.04 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP A 623 HIS 0.004 0.001 HIS B 304 PHE 0.035 0.002 PHE C 172 TYR 0.028 0.002 TYR D 105 ARG 0.006 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03936 ( 912) hydrogen bonds : angle 5.15388 ( 2664) SS BOND : bond 0.00636 ( 3) SS BOND : angle 5.24878 ( 6) covalent geometry : bond 0.00491 (17038) covalent geometry : angle 0.68452 (23020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 658 time to evaluate : 2.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9068 (tptp) cc_final: 0.8653 (tppt) REVERT: A 12 LEU cc_start: 0.9568 (mt) cc_final: 0.9303 (mt) REVERT: A 66 GLU cc_start: 0.8426 (tp30) cc_final: 0.8165 (tp30) REVERT: A 117 ARG cc_start: 0.8503 (mmt180) cc_final: 0.8244 (mtt-85) REVERT: A 157 LEU cc_start: 0.9304 (tp) cc_final: 0.9029 (tp) REVERT: A 191 GLN cc_start: 0.8879 (mm-40) cc_final: 0.8328 (mm-40) REVERT: A 243 ARG cc_start: 0.7231 (tpt-90) cc_final: 0.7019 (tpt-90) REVERT: A 250 TYR cc_start: 0.8221 (m-80) cc_final: 0.7884 (m-80) REVERT: A 256 ARG cc_start: 0.9244 (tmt-80) cc_final: 0.8619 (tmt-80) REVERT: A 290 GLU cc_start: 0.9067 (tm-30) cc_final: 0.8675 (tm-30) REVERT: A 291 LEU cc_start: 0.9493 (mm) cc_final: 0.9111 (mm) REVERT: A 301 PHE cc_start: 0.8996 (m-80) cc_final: 0.8636 (m-80) REVERT: A 338 ASN cc_start: 0.9268 (t0) cc_final: 0.8057 (t0) REVERT: A 341 LYS cc_start: 0.9638 (mttt) cc_final: 0.9424 (mttt) REVERT: A 362 ASP cc_start: 0.8050 (m-30) cc_final: 0.7752 (m-30) REVERT: A 367 VAL cc_start: 0.9543 (m) cc_final: 0.9285 (p) REVERT: A 421 GLU cc_start: 0.8520 (pp20) cc_final: 0.8158 (pp20) REVERT: A 490 THR cc_start: 0.8571 (p) cc_final: 0.7460 (t) REVERT: A 491 PHE cc_start: 0.9551 (t80) cc_final: 0.9228 (t80) REVERT: A 501 GLN cc_start: 0.9318 (tt0) cc_final: 0.8194 (tm-30) REVERT: A 505 GLU cc_start: 0.8624 (pt0) cc_final: 0.8113 (pt0) REVERT: A 515 ASP cc_start: 0.8895 (m-30) cc_final: 0.8525 (m-30) REVERT: A 590 SER cc_start: 0.9489 (t) cc_final: 0.9266 (p) REVERT: A 615 MET cc_start: 0.9019 (mmm) cc_final: 0.8609 (mmm) REVERT: A 645 GLN cc_start: 0.8748 (tp40) cc_final: 0.8528 (tp-100) REVERT: A 655 THR cc_start: 0.9149 (m) cc_final: 0.8709 (t) REVERT: B 30 LYS cc_start: 0.9292 (tmtt) cc_final: 0.9063 (tptt) REVERT: B 40 TYR cc_start: 0.9263 (t80) cc_final: 0.8943 (t80) REVERT: B 87 LYS cc_start: 0.9149 (tppt) cc_final: 0.8632 (tptp) REVERT: B 112 LYS cc_start: 0.9409 (mmpt) cc_final: 0.9193 (mmmt) REVERT: B 127 LEU cc_start: 0.9789 (mt) cc_final: 0.9578 (mm) REVERT: B 129 PHE cc_start: 0.9114 (m-10) cc_final: 0.8890 (m-80) REVERT: B 147 GLN cc_start: 0.9177 (mt0) cc_final: 0.8687 (mt0) REVERT: B 184 ARG cc_start: 0.9504 (tpp80) cc_final: 0.9217 (tpp80) REVERT: B 186 ILE cc_start: 0.9555 (mt) cc_final: 0.9313 (mt) REVERT: B 190 MET cc_start: 0.9279 (mtm) cc_final: 0.8979 (mtm) REVERT: B 216 VAL cc_start: 0.9078 (t) cc_final: 0.8791 (p) REVERT: B 231 ASP cc_start: 0.8363 (t70) cc_final: 0.6936 (t70) REVERT: B 232 ASN cc_start: 0.9140 (m-40) cc_final: 0.8694 (m110) REVERT: B 235 ARG cc_start: 0.8761 (mtm-85) cc_final: 0.7731 (mtm-85) REVERT: B 257 ASP cc_start: 0.8324 (m-30) cc_final: 0.7347 (m-30) REVERT: B 260 ASP cc_start: 0.9191 (m-30) cc_final: 0.8742 (p0) REVERT: B 335 GLU cc_start: 0.7932 (tm-30) cc_final: 0.7722 (tm-30) REVERT: B 348 MET cc_start: 0.8972 (ppp) cc_final: 0.8448 (ppp) REVERT: B 349 LEU cc_start: 0.9373 (mt) cc_final: 0.8649 (mt) REVERT: B 358 ILE cc_start: 0.9575 (mm) cc_final: 0.9179 (tp) REVERT: B 378 PHE cc_start: 0.8844 (p90) cc_final: 0.8393 (p90) REVERT: B 394 TYR cc_start: 0.8863 (m-80) cc_final: 0.8642 (m-80) REVERT: B 402 GLU cc_start: 0.8286 (mp0) cc_final: 0.7631 (mp0) REVERT: B 415 ASN cc_start: 0.9082 (t0) cc_final: 0.8872 (t0) REVERT: B 425 ILE cc_start: 0.8848 (mt) cc_final: 0.7977 (mt) REVERT: B 426 GLU cc_start: 0.8889 (tp30) cc_final: 0.8563 (tp30) REVERT: B 427 LYS cc_start: 0.9117 (ptpp) cc_final: 0.8861 (ptpp) REVERT: B 437 THR cc_start: 0.9564 (m) cc_final: 0.9177 (m) REVERT: B 494 MET cc_start: 0.9058 (ttt) cc_final: 0.8794 (ttt) REVERT: B 570 MET cc_start: 0.8525 (tpp) cc_final: 0.6698 (tpp) REVERT: B 599 GLU cc_start: 0.9149 (pm20) cc_final: 0.8810 (pm20) REVERT: B 656 LEU cc_start: 0.9259 (mt) cc_final: 0.9028 (mt) REVERT: C 17 PHE cc_start: 0.9054 (p90) cc_final: 0.8353 (p90) REVERT: C 20 MET cc_start: 0.9381 (ppp) cc_final: 0.9140 (ppp) REVERT: C 21 PHE cc_start: 0.9087 (m-80) cc_final: 0.8548 (m-80) REVERT: C 56 MET cc_start: 0.1122 (ptm) cc_final: 0.0457 (ttp) REVERT: C 74 MET cc_start: 0.9247 (mpp) cc_final: 0.8932 (mpp) REVERT: C 89 VAL cc_start: 0.7653 (t) cc_final: 0.7273 (m) REVERT: C 95 MET cc_start: 0.8644 (ttp) cc_final: 0.8112 (ttp) REVERT: C 157 MET cc_start: 0.9353 (mtm) cc_final: 0.8962 (ptp) REVERT: C 174 TYR cc_start: 0.8835 (t80) cc_final: 0.8213 (t80) REVERT: C 226 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8458 (mt-10) REVERT: C 231 LEU cc_start: 0.8960 (mt) cc_final: 0.8756 (mt) REVERT: C 270 ASN cc_start: 0.9269 (m-40) cc_final: 0.9057 (m-40) REVERT: C 274 ASP cc_start: 0.9057 (p0) cc_final: 0.8699 (p0) REVERT: D 25 ASN cc_start: 0.9491 (m-40) cc_final: 0.9277 (m-40) REVERT: D 92 PHE cc_start: 0.7153 (t80) cc_final: 0.6933 (t80) REVERT: D 137 MET cc_start: 0.8491 (mmp) cc_final: 0.8019 (mtt) REVERT: D 185 MET cc_start: 0.6537 (ptm) cc_final: 0.6303 (ptm) REVERT: D 238 ASN cc_start: 0.8523 (m110) cc_final: 0.8078 (m110) REVERT: E 24 PHE cc_start: 0.9220 (m-10) cc_final: 0.8843 (m-80) REVERT: E 46 MET cc_start: 0.8144 (tpp) cc_final: 0.7935 (tpp) REVERT: E 60 ASN cc_start: 0.9402 (t0) cc_final: 0.9169 (t0) REVERT: E 67 TYR cc_start: 0.8651 (m-80) cc_final: 0.8439 (m-80) outliers start: 1 outliers final: 0 residues processed: 658 average time/residue: 0.3235 time to fit residues: 322.9073 Evaluate side-chains 559 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 2.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 1.9990 chunk 85 optimal weight: 1.9990 chunk 184 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 78 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 147 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 113 optimal weight: 4.9990 chunk 109 optimal weight: 4.9990 chunk 122 optimal weight: 0.3980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.132546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.094365 restraints weight = 42490.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.098060 restraints weight = 21916.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.100412 restraints weight = 13535.189| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7588 moved from start: 0.7208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17041 Z= 0.152 Angle : 0.663 10.067 23026 Z= 0.344 Chirality : 0.045 0.271 2464 Planarity : 0.004 0.050 2931 Dihedral : 9.924 143.954 2325 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.74 (0.19), residues: 2012 helix: 1.01 (0.15), residues: 1130 sheet: -0.26 (0.41), residues: 157 loop : 0.02 (0.24), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 623 HIS 0.006 0.001 HIS C 201 PHE 0.025 0.002 PHE C 172 TYR 0.030 0.002 TYR A 571 ARG 0.005 0.001 ARG B 184 Details of bonding type rmsd hydrogen bonds : bond 0.03844 ( 912) hydrogen bonds : angle 5.15135 ( 2664) SS BOND : bond 0.00906 ( 3) SS BOND : angle 4.82543 ( 6) covalent geometry : bond 0.00346 (17038) covalent geometry : angle 0.65828 (23020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 650 time to evaluate : 1.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9092 (tptp) cc_final: 0.8647 (tppt) REVERT: A 12 LEU cc_start: 0.9577 (mt) cc_final: 0.9253 (mt) REVERT: A 66 GLU cc_start: 0.8448 (tp30) cc_final: 0.8177 (tp30) REVERT: A 117 ARG cc_start: 0.8395 (mmt180) cc_final: 0.8106 (mtt-85) REVERT: A 150 GLN cc_start: 0.8659 (tp40) cc_final: 0.8354 (tp40) REVERT: A 187 ASP cc_start: 0.8539 (t70) cc_final: 0.8276 (t0) REVERT: A 209 LYS cc_start: 0.9349 (tttm) cc_final: 0.9131 (tttm) REVERT: A 228 LYS cc_start: 0.9089 (tptt) cc_final: 0.8590 (mptt) REVERT: A 230 LEU cc_start: 0.9707 (mt) cc_final: 0.9503 (mt) REVERT: A 234 PHE cc_start: 0.9440 (m-80) cc_final: 0.9223 (m-80) REVERT: A 250 TYR cc_start: 0.8172 (m-80) cc_final: 0.7874 (m-80) REVERT: A 254 PHE cc_start: 0.8949 (m-80) cc_final: 0.8586 (m-80) REVERT: A 256 ARG cc_start: 0.9208 (tmt-80) cc_final: 0.8995 (ttp80) REVERT: A 257 ASP cc_start: 0.8759 (m-30) cc_final: 0.7816 (m-30) REVERT: A 290 GLU cc_start: 0.9025 (tm-30) cc_final: 0.8568 (tm-30) REVERT: A 291 LEU cc_start: 0.9512 (mm) cc_final: 0.8977 (mm) REVERT: A 301 PHE cc_start: 0.8949 (m-80) cc_final: 0.8656 (m-80) REVERT: A 349 LEU cc_start: 0.9569 (tt) cc_final: 0.9056 (tt) REVERT: A 362 ASP cc_start: 0.7954 (m-30) cc_final: 0.7518 (m-30) REVERT: A 421 GLU cc_start: 0.8516 (pp20) cc_final: 0.8232 (pp20) REVERT: A 490 THR cc_start: 0.8517 (p) cc_final: 0.7354 (t) REVERT: A 491 PHE cc_start: 0.9530 (t80) cc_final: 0.9085 (t80) REVERT: A 493 MET cc_start: 0.8013 (tmm) cc_final: 0.7617 (tmm) REVERT: A 501 GLN cc_start: 0.9235 (tt0) cc_final: 0.8723 (tm-30) REVERT: A 505 GLU cc_start: 0.8698 (pt0) cc_final: 0.8276 (pt0) REVERT: A 515 ASP cc_start: 0.8810 (m-30) cc_final: 0.8387 (m-30) REVERT: A 615 MET cc_start: 0.8948 (mmm) cc_final: 0.8616 (mmm) REVERT: A 645 GLN cc_start: 0.9042 (tp40) cc_final: 0.8723 (tp40) REVERT: A 655 THR cc_start: 0.9093 (m) cc_final: 0.8572 (t) REVERT: B 10 ILE cc_start: 0.9561 (mt) cc_final: 0.9062 (mt) REVERT: B 30 LYS cc_start: 0.9304 (tmtt) cc_final: 0.9072 (tptt) REVERT: B 87 LYS cc_start: 0.9103 (tppt) cc_final: 0.8609 (tptp) REVERT: B 112 LYS cc_start: 0.9366 (mmpt) cc_final: 0.9157 (mmmt) REVERT: B 120 ASP cc_start: 0.8793 (m-30) cc_final: 0.8494 (m-30) REVERT: B 127 LEU cc_start: 0.9780 (mt) cc_final: 0.9500 (mm) REVERT: B 129 PHE cc_start: 0.9133 (m-10) cc_final: 0.8849 (m-80) REVERT: B 147 GLN cc_start: 0.9123 (mt0) cc_final: 0.8634 (mt0) REVERT: B 150 GLN cc_start: 0.9514 (tp40) cc_final: 0.9279 (tp40) REVERT: B 184 ARG cc_start: 0.9530 (tpp80) cc_final: 0.9255 (tpp80) REVERT: B 186 ILE cc_start: 0.9583 (mt) cc_final: 0.9322 (mt) REVERT: B 190 MET cc_start: 0.9248 (mtm) cc_final: 0.8949 (mtm) REVERT: B 216 VAL cc_start: 0.8994 (t) cc_final: 0.8719 (p) REVERT: B 231 ASP cc_start: 0.8418 (t70) cc_final: 0.7123 (t70) REVERT: B 232 ASN cc_start: 0.9091 (m-40) cc_final: 0.8617 (m110) REVERT: B 235 ARG cc_start: 0.8819 (mtm-85) cc_final: 0.7884 (mtm-85) REVERT: B 335 GLU cc_start: 0.7967 (tm-30) cc_final: 0.7720 (tm-30) REVERT: B 348 MET cc_start: 0.8998 (ppp) cc_final: 0.8454 (ppp) REVERT: B 349 LEU cc_start: 0.9331 (mt) cc_final: 0.8603 (mt) REVERT: B 378 PHE cc_start: 0.8833 (p90) cc_final: 0.8395 (p90) REVERT: B 394 TYR cc_start: 0.8850 (m-80) cc_final: 0.8583 (m-80) REVERT: B 402 GLU cc_start: 0.8325 (mp0) cc_final: 0.7651 (mp0) REVERT: B 426 GLU cc_start: 0.8972 (tp30) cc_final: 0.8691 (tp30) REVERT: B 437 THR cc_start: 0.9554 (m) cc_final: 0.9202 (m) REVERT: B 475 ASN cc_start: 0.8872 (m-40) cc_final: 0.8592 (m110) REVERT: B 570 MET cc_start: 0.8490 (tpp) cc_final: 0.6620 (tpp) REVERT: B 598 MET cc_start: 0.8378 (mtp) cc_final: 0.8044 (mtp) REVERT: B 599 GLU cc_start: 0.8971 (pm20) cc_final: 0.8684 (pm20) REVERT: B 623 TRP cc_start: 0.8850 (t-100) cc_final: 0.8455 (t-100) REVERT: B 637 VAL cc_start: 0.8949 (t) cc_final: 0.8521 (t) REVERT: B 670 ILE cc_start: 0.9280 (mt) cc_final: 0.9056 (mt) REVERT: B 683 TYR cc_start: 0.7878 (t80) cc_final: 0.6914 (t80) REVERT: C 17 PHE cc_start: 0.9056 (p90) cc_final: 0.8345 (p90) REVERT: C 20 MET cc_start: 0.9432 (ppp) cc_final: 0.9213 (ppp) REVERT: C 21 PHE cc_start: 0.9100 (m-80) cc_final: 0.8551 (m-80) REVERT: C 56 MET cc_start: 0.0674 (ptm) cc_final: -0.0035 (ttp) REVERT: C 74 MET cc_start: 0.9247 (mpp) cc_final: 0.8817 (mpp) REVERT: C 95 MET cc_start: 0.8602 (ttp) cc_final: 0.8082 (ttp) REVERT: C 157 MET cc_start: 0.9462 (mtm) cc_final: 0.8924 (ptp) REVERT: C 174 TYR cc_start: 0.8897 (t80) cc_final: 0.8402 (t80) REVERT: C 226 GLU cc_start: 0.8751 (mt-10) cc_final: 0.8411 (mt-10) REVERT: C 231 LEU cc_start: 0.8955 (mt) cc_final: 0.8749 (mt) REVERT: C 274 ASP cc_start: 0.9095 (p0) cc_final: 0.8764 (p0) REVERT: D 25 ASN cc_start: 0.9471 (m-40) cc_final: 0.9270 (m-40) REVERT: D 128 ASN cc_start: 0.8534 (t0) cc_final: 0.8186 (t0) REVERT: D 137 MET cc_start: 0.8473 (mmp) cc_final: 0.8069 (mtt) REVERT: E 24 PHE cc_start: 0.9286 (m-10) cc_final: 0.8922 (m-80) REVERT: E 25 TRP cc_start: 0.8152 (p-90) cc_final: 0.7783 (p-90) REVERT: E 60 ASN cc_start: 0.9378 (t0) cc_final: 0.9126 (t0) REVERT: E 67 TYR cc_start: 0.8609 (m-80) cc_final: 0.8400 (m-80) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.2804 time to fit residues: 274.9218 Evaluate side-chains 557 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 557 time to evaluate : 2.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 173 optimal weight: 9.9990 chunk 64 optimal weight: 0.7980 chunk 105 optimal weight: 7.9990 chunk 106 optimal weight: 0.8980 chunk 73 optimal weight: 0.0060 chunk 56 optimal weight: 0.6980 chunk 198 optimal weight: 0.0570 chunk 121 optimal weight: 0.9980 chunk 102 optimal weight: 6.9990 overall best weight: 0.4914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.137664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.101025 restraints weight = 42756.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.104297 restraints weight = 22885.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.106704 restraints weight = 14745.871| |-----------------------------------------------------------------------------| r_work (final): 0.3338 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3342 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3342 r_free = 0.3342 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3341 r_free = 0.3341 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3341 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.7430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 17041 Z= 0.135 Angle : 0.659 9.216 23026 Z= 0.342 Chirality : 0.045 0.221 2464 Planarity : 0.004 0.051 2931 Dihedral : 9.735 141.255 2325 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.71 (0.19), residues: 2012 helix: 0.99 (0.15), residues: 1147 sheet: -0.25 (0.41), residues: 157 loop : -0.04 (0.24), residues: 708 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 124 HIS 0.005 0.001 HIS B 438 PHE 0.045 0.002 PHE C 172 TYR 0.025 0.002 TYR C 173 ARG 0.008 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.03831 ( 912) hydrogen bonds : angle 5.08299 ( 2664) SS BOND : bond 0.00721 ( 3) SS BOND : angle 4.62541 ( 6) covalent geometry : bond 0.00301 (17038) covalent geometry : angle 0.65487 (23020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 661 time to evaluate : 1.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 8 LYS cc_start: 0.9060 (tptp) cc_final: 0.8763 (tppt) REVERT: A 66 GLU cc_start: 0.8428 (tp30) cc_final: 0.8178 (tp30) REVERT: A 117 ARG cc_start: 0.8348 (mmt180) cc_final: 0.8057 (mtt-85) REVERT: A 161 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7682 (ptm160) REVERT: A 184 ARG cc_start: 0.9314 (mmm-85) cc_final: 0.8850 (mmm-85) REVERT: A 187 ASP cc_start: 0.8688 (t70) cc_final: 0.8310 (t0) REVERT: A 209 LYS cc_start: 0.9333 (tttm) cc_final: 0.9103 (tttm) REVERT: A 228 LYS cc_start: 0.9111 (tptt) cc_final: 0.8603 (mptt) REVERT: A 234 PHE cc_start: 0.9312 (m-80) cc_final: 0.9073 (m-80) REVERT: A 250 TYR cc_start: 0.8147 (m-80) cc_final: 0.7903 (m-80) REVERT: A 252 ASN cc_start: 0.9330 (t0) cc_final: 0.9115 (t0) REVERT: A 256 ARG cc_start: 0.9257 (tmt-80) cc_final: 0.8995 (ttp80) REVERT: A 257 ASP cc_start: 0.8729 (m-30) cc_final: 0.7612 (m-30) REVERT: A 286 ASP cc_start: 0.8814 (m-30) cc_final: 0.8464 (m-30) REVERT: A 290 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8561 (tm-30) REVERT: A 291 LEU cc_start: 0.9480 (mm) cc_final: 0.8939 (mm) REVERT: A 301 PHE cc_start: 0.8969 (m-80) cc_final: 0.8566 (m-80) REVERT: A 362 ASP cc_start: 0.7763 (m-30) cc_final: 0.7490 (m-30) REVERT: A 366 LYS cc_start: 0.9380 (mmtp) cc_final: 0.9147 (mmtm) REVERT: A 367 VAL cc_start: 0.9484 (m) cc_final: 0.9269 (p) REVERT: A 420 MET cc_start: 0.8679 (tpp) cc_final: 0.8441 (mtp) REVERT: A 421 GLU cc_start: 0.8373 (pp20) cc_final: 0.8084 (pp20) REVERT: A 456 LYS cc_start: 0.9035 (ptpp) cc_final: 0.8763 (ptpp) REVERT: A 490 THR cc_start: 0.8475 (p) cc_final: 0.7456 (t) REVERT: A 491 PHE cc_start: 0.9462 (t80) cc_final: 0.9133 (t80) REVERT: A 493 MET cc_start: 0.7899 (tmm) cc_final: 0.7502 (tmm) REVERT: A 498 TYR cc_start: 0.8677 (m-80) cc_final: 0.8228 (m-80) REVERT: A 501 GLN cc_start: 0.9208 (tt0) cc_final: 0.8383 (tm-30) REVERT: A 505 GLU cc_start: 0.8677 (pt0) cc_final: 0.8251 (pt0) REVERT: A 515 ASP cc_start: 0.8721 (m-30) cc_final: 0.8263 (m-30) REVERT: A 561 LEU cc_start: 0.9112 (tp) cc_final: 0.8805 (tp) REVERT: A 615 MET cc_start: 0.8844 (mmm) cc_final: 0.8579 (mmm) REVERT: A 645 GLN cc_start: 0.9058 (tp40) cc_final: 0.8757 (tp40) REVERT: A 655 THR cc_start: 0.9001 (m) cc_final: 0.8669 (t) REVERT: A 661 THR cc_start: 0.9603 (p) cc_final: 0.9108 (p) REVERT: A 662 MET cc_start: 0.7841 (ptp) cc_final: 0.7638 (pmm) REVERT: A 686 ARG cc_start: 0.7840 (mtp180) cc_final: 0.7585 (mtp180) REVERT: B 30 LYS cc_start: 0.9300 (tmtt) cc_final: 0.9072 (tptt) REVERT: B 87 LYS cc_start: 0.9071 (tppt) cc_final: 0.8575 (tptp) REVERT: B 112 LYS cc_start: 0.9388 (mmpt) cc_final: 0.9164 (mmmt) REVERT: B 120 ASP cc_start: 0.8787 (m-30) cc_final: 0.8482 (m-30) REVERT: B 127 LEU cc_start: 0.9769 (mt) cc_final: 0.9480 (mm) REVERT: B 129 PHE cc_start: 0.9173 (m-10) cc_final: 0.8890 (m-80) REVERT: B 147 GLN cc_start: 0.9056 (mt0) cc_final: 0.8341 (mt0) REVERT: B 150 GLN cc_start: 0.9551 (tp40) cc_final: 0.9346 (tp-100) REVERT: B 184 ARG cc_start: 0.9540 (tpp80) cc_final: 0.9242 (tpp80) REVERT: B 186 ILE cc_start: 0.9542 (mt) cc_final: 0.9332 (mt) REVERT: B 190 MET cc_start: 0.9312 (mtm) cc_final: 0.8999 (mtm) REVERT: B 204 SER cc_start: 0.8258 (t) cc_final: 0.7705 (t) REVERT: B 217 GLU cc_start: 0.9306 (tm-30) cc_final: 0.9027 (tm-30) REVERT: B 231 ASP cc_start: 0.8404 (t70) cc_final: 0.7131 (t70) REVERT: B 232 ASN cc_start: 0.9087 (m-40) cc_final: 0.8546 (m110) REVERT: B 235 ARG cc_start: 0.8825 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: B 335 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7637 (tm-30) REVERT: B 348 MET cc_start: 0.9004 (ppp) cc_final: 0.8449 (ppp) REVERT: B 349 LEU cc_start: 0.9298 (mt) cc_final: 0.8573 (mt) REVERT: B 378 PHE cc_start: 0.8837 (p90) cc_final: 0.8400 (p90) REVERT: B 415 ASN cc_start: 0.9018 (t0) cc_final: 0.8412 (t0) REVERT: B 418 ASN cc_start: 0.8463 (m-40) cc_final: 0.8130 (m-40) REVERT: B 426 GLU cc_start: 0.8983 (tp30) cc_final: 0.8714 (tp30) REVERT: B 427 LYS cc_start: 0.9119 (ptpp) cc_final: 0.8788 (ptpp) REVERT: B 437 THR cc_start: 0.9477 (m) cc_final: 0.9166 (m) REVERT: B 475 ASN cc_start: 0.8814 (m-40) cc_final: 0.8605 (m110) REVERT: B 570 MET cc_start: 0.8464 (tpp) cc_final: 0.6695 (tpp) REVERT: B 599 GLU cc_start: 0.8960 (pm20) cc_final: 0.8742 (pm20) REVERT: B 623 TRP cc_start: 0.8874 (t-100) cc_final: 0.8422 (t-100) REVERT: B 656 LEU cc_start: 0.9166 (mt) cc_final: 0.8942 (mt) REVERT: B 670 ILE cc_start: 0.9301 (mt) cc_final: 0.9071 (mt) REVERT: C 17 PHE cc_start: 0.9062 (p90) cc_final: 0.8364 (p90) REVERT: C 20 MET cc_start: 0.9454 (ppp) cc_final: 0.9214 (ppp) REVERT: C 21 PHE cc_start: 0.9077 (m-80) cc_final: 0.8464 (m-80) REVERT: C 56 MET cc_start: 0.0594 (ptm) cc_final: -0.0103 (ttp) REVERT: C 68 GLU cc_start: 0.8879 (mp0) cc_final: 0.8391 (pm20) REVERT: C 95 MET cc_start: 0.8646 (ttp) cc_final: 0.8212 (ttp) REVERT: C 157 MET cc_start: 0.9457 (mtm) cc_final: 0.8911 (ptp) REVERT: C 174 TYR cc_start: 0.8910 (t80) cc_final: 0.8387 (t80) REVERT: C 226 GLU cc_start: 0.8740 (mt-10) cc_final: 0.8401 (mt-10) REVERT: C 231 LEU cc_start: 0.8950 (mt) cc_final: 0.8742 (mt) REVERT: C 274 ASP cc_start: 0.9076 (p0) cc_final: 0.8827 (p0) REVERT: D 25 ASN cc_start: 0.9505 (m-40) cc_final: 0.9300 (m-40) REVERT: D 92 PHE cc_start: 0.6971 (t80) cc_final: 0.6708 (t80) REVERT: D 137 MET cc_start: 0.8478 (mmp) cc_final: 0.8091 (mtt) REVERT: D 238 ASN cc_start: 0.8501 (m110) cc_final: 0.8013 (m110) REVERT: E 24 PHE cc_start: 0.9316 (m-10) cc_final: 0.9049 (m-80) REVERT: E 25 TRP cc_start: 0.8213 (p-90) cc_final: 0.7959 (p-90) REVERT: E 60 ASN cc_start: 0.9352 (t0) cc_final: 0.9103 (t0) REVERT: E 67 TYR cc_start: 0.8643 (m-80) cc_final: 0.8427 (m-80) outliers start: 0 outliers final: 0 residues processed: 661 average time/residue: 0.3176 time to fit residues: 318.2569 Evaluate side-chains 570 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 570 time to evaluate : 2.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 198 optimal weight: 20.0000 chunk 146 optimal weight: 6.9990 chunk 165 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 chunk 173 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 124 optimal weight: 3.9990 chunk 144 optimal weight: 20.0000 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 61 ASN B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 132 GLN ** C 238 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 132 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.127764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091752 restraints weight = 43749.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.094937 restraints weight = 22996.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.097136 restraints weight = 14775.294| |-----------------------------------------------------------------------------| r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3220 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3220 r_free = 0.3220 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3220 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.7579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.083 17041 Z= 0.266 Angle : 0.751 12.730 23026 Z= 0.391 Chirality : 0.047 0.224 2464 Planarity : 0.004 0.049 2931 Dihedral : 10.064 150.549 2325 Min Nonbonded Distance : 1.750 Molprobity Statistics. All-atom Clashscore : 19.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % 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: 0.45 (0.18), residues: 2012 helix: 0.79 (0.15), residues: 1150 sheet: -0.42 (0.41), residues: 161 loop : -0.16 (0.24), residues: 701 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 623 HIS 0.006 0.001 HIS C 201 PHE 0.037 0.003 PHE C 172 TYR 0.028 0.002 TYR D 105 ARG 0.009 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.04161 ( 912) hydrogen bonds : angle 5.35614 ( 2664) SS BOND : bond 0.00701 ( 3) SS BOND : angle 4.85353 ( 6) covalent geometry : bond 0.00576 (17038) covalent geometry : angle 0.74652 (23020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8049.93 seconds wall clock time: 141 minutes 44.08 seconds (8504.08 seconds total)