Starting phenix.real_space_refine on Sun Aug 24 03:05:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9by0_45016/08_2025/9by0_45016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9by0_45016/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2025/9by0_45016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2025/9by0_45016.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2025/9by0_45016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9by0_45016/08_2025/9by0_45016.map" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 3.22, per 1000 atoms: 0.19 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: 1.06 Conformation dependent library (CDL) restraints added in 630.1 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.49 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: 2.48 Time building geometry restraints manager: 1.49 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: 1.010 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: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.440 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.030 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.240 ------------------------------------------------------------------------------- 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 : 10.05 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.007 0.000 ARG A 331 TYR 0.029 0.002 TYR E 67 PHE 0.120 0.003 PHE B 624 TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 Details of bonding type rmsd covalent geometry : bond 0.00602 (17038) covalent geometry : angle 0.83524 (23020) SS BOND : bond 0.36331 ( 3) SS BOND : angle 6.07971 ( 6) hydrogen bonds : bond 0.16741 ( 912) hydrogen bonds : angle 6.70349 ( 2664) *********************** 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 : 0.540 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: A 59 VAL cc_start: 0.8664 (t) cc_final: 0.8421 (p) REVERT: A 68 PHE cc_start: 0.7989 (p90) cc_final: 0.7656 (p90) REVERT: A 171 PHE cc_start: 0.8288 (m-80) cc_final: 0.7965 (m-80) REVERT: A 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8666 (t0) REVERT: A 367 VAL cc_start: 0.8707 (m) cc_final: 0.8304 (p) REVERT: A 378 PHE cc_start: 0.8293 (p90) cc_final: 0.7922 (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: 0.9184 (t) REVERT: B 17 MET cc_start: 0.7011 (mmm) cc_final: 0.6211 (mmm) REVERT: B 41 ILE cc_start: 0.8797 (mm) cc_final: 0.8315 (mt) REVERT: B 46 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8141 (m) REVERT: B 51 LEU cc_start: 0.7905 (tp) cc_final: 0.7647 (tp) REVERT: B 127 LEU cc_start: 0.9293 (mt) cc_final: 0.9057 (mt) REVERT: B 129 PHE cc_start: 0.7800 (m-10) cc_final: 0.7475 (m-80) REVERT: B 177 ASP cc_start: 0.8336 (t0) cc_final: 0.7996 (t0) REVERT: B 204 SER cc_start: 0.8620 (m) cc_final: 0.8384 (t) REVERT: B 230 LEU cc_start: 0.9308 (mt) cc_final: 0.9078 (mt) REVERT: B 315 ASP cc_start: 0.8578 (p0) cc_final: 0.8274 (t0) REVERT: B 317 MET cc_start: 0.8078 (mtp) cc_final: 0.7842 (mtt) REVERT: B 322 MET cc_start: 0.7356 (mmm) cc_final: 0.6943 (mmm) REVERT: B 349 LEU cc_start: 0.8462 (mt) cc_final: 0.8147 (mp) REVERT: B 364 VAL cc_start: 0.8818 (t) cc_final: 0.8605 (t) REVERT: B 384 GLU cc_start: 0.8215 (pp20) cc_final: 0.7611 (pm20) REVERT: B 385 VAL cc_start: 0.8660 (t) cc_final: 0.8388 (t) REVERT: B 500 ILE cc_start: 0.9353 (mt) cc_final: 0.8771 (mt) REVERT: B 531 TYR cc_start: 0.6004 (m-80) cc_final: 0.5677 (m-80) REVERT: B 550 MET cc_start: 0.7101 (mtm) cc_final: 0.6595 (mtp) REVERT: B 574 TYR cc_start: 0.8035 (m-80) cc_final: 0.7822 (m-80) REVERT: B 576 LEU cc_start: 0.8710 (mt) cc_final: 0.8321 (mt) REVERT: B 626 TYR cc_start: 0.6498 (m-80) cc_final: 0.6085 (m-80) REVERT: B 644 ILE cc_start: 0.8828 (mt) cc_final: 0.8597 (mt) REVERT: B 687 THR cc_start: 0.7230 (p) cc_final: 0.6962 (p) REVERT: C 89 VAL cc_start: 0.6220 (t) cc_final: 0.5271 (t) REVERT: C 101 HIS cc_start: 0.5472 (m170) cc_final: 0.4817 (m-70) REVERT: C 131 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6054 (tp) REVERT: C 153 LEU cc_start: 0.7009 (tp) cc_final: 0.6712 (tp) REVERT: C 163 LEU cc_start: 0.6154 (tt) cc_final: 0.5806 (tp) REVERT: C 268 LEU cc_start: 0.4343 (mt) cc_final: 0.4035 (mt) REVERT: D 185 MET cc_start: 0.6866 (mmm) cc_final: 0.6543 (tpp) REVERT: D 265 ASN cc_start: 0.4744 (m-40) cc_final: 0.4463 (m110) REVERT: E 25 TRP cc_start: 0.8230 (p-90) cc_final: 0.7939 (p-90) REVERT: E 78 LEU cc_start: 0.6579 (mp) cc_final: 0.5540 (tt) outliers start: 25 outliers final: 4 residues processed: 948 average time/residue: 0.1235 time to fit residues: 172.6608 Evaluate side-chains 648 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 642 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 9.9990 chunk 91 optimal weight: 0.4980 overall best weight: 1.6988 ------------------------------------------------------------------------------- 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 180 ASN ** 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 320 ASN B 370 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 216 GLN D 71 ASN D 80 HIS ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 127 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3816 r_free = 0.3816 target = 0.134186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.097622 restraints weight = 41451.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101039 restraints weight = 22140.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.103381 restraints weight = 14164.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.104851 restraints weight = 10137.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.106017 restraints weight = 7927.500| |-----------------------------------------------------------------------------| r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3364 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3364 r_free = 0.3364 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3362 r_free = 0.3362 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3362 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7255 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.105 17041 Z= 0.191 Angle : 0.684 14.880 23026 Z= 0.359 Chirality : 0.044 0.238 2464 Planarity : 0.004 0.041 2931 Dihedral : 10.558 147.648 2325 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.34 % Allowed : 2.63 % Favored : 97.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.18), residues: 2012 helix: 1.29 (0.15), residues: 1156 sheet: -0.26 (0.38), residues: 163 loop : 0.56 (0.24), residues: 693 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 235 TYR 0.036 0.002 TYR C 174 PHE 0.029 0.002 PHE C 168 TRP 0.020 0.002 TRP B 558 HIS 0.009 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00414 (17038) covalent geometry : angle 0.67222 (23020) SS BOND : bond 0.00411 ( 3) SS BOND : angle 7.81498 ( 6) hydrogen bonds : bond 0.04783 ( 912) hydrogen bonds : angle 5.11377 ( 2664) *********************** 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 746 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 740 time to evaluate : 0.635 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: A 145 ILE cc_start: 0.9022 (tp) cc_final: 0.8775 (tp) REVERT: A 147 GLN cc_start: 0.8483 (tp-100) cc_final: 0.7936 (tp40) REVERT: A 223 VAL cc_start: 0.9434 (m) cc_final: 0.9138 (p) REVERT: A 227 MET cc_start: 0.9369 (mtm) cc_final: 0.9116 (mtm) REVERT: A 338 ASN cc_start: 0.9546 (t0) cc_final: 0.7927 (t0) REVERT: A 341 LYS cc_start: 0.9687 (mmtp) cc_final: 0.9375 (mmtp) REVERT: A 346 LEU cc_start: 0.9501 (mt) cc_final: 0.9292 (mt) REVERT: A 367 VAL cc_start: 0.9562 (m) cc_final: 0.9285 (p) REVERT: A 390 GLN cc_start: 0.8392 (mt0) cc_final: 0.8187 (mt0) REVERT: A 421 GLU cc_start: 0.8240 (pp20) cc_final: 0.7873 (pp20) REVERT: A 475 ASN cc_start: 0.8276 (m110) cc_final: 0.7849 (m110) REVERT: A 509 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8406 (tm-30) REVERT: A 518 GLU cc_start: 0.8894 (pp20) cc_final: 0.8568 (pp20) REVERT: A 528 PHE cc_start: 0.8278 (m-10) cc_final: 0.7838 (m-80) REVERT: A 558 TRP cc_start: 0.8820 (m100) cc_final: 0.8473 (m100) REVERT: A 615 MET cc_start: 0.8853 (mmm) cc_final: 0.8494 (mmm) REVERT: A 639 ASP cc_start: 0.8907 (m-30) cc_final: 0.8615 (m-30) REVERT: A 658 LEU cc_start: 0.9569 (mp) cc_final: 0.9311 (mp) REVERT: B 51 LEU cc_start: 0.9263 (tp) cc_final: 0.9061 (tp) REVERT: B 127 LEU cc_start: 0.9775 (mt) cc_final: 0.9483 (mm) REVERT: B 135 GLU cc_start: 0.9149 (mp0) cc_final: 0.8812 (pm20) REVERT: B 147 GLN cc_start: 0.9013 (mt0) cc_final: 0.8578 (mt0) REVERT: B 156 PHE cc_start: 0.9282 (t80) cc_final: 0.9037 (t80) REVERT: B 186 ILE cc_start: 0.9639 (mt) cc_final: 0.9076 (mt) REVERT: B 190 MET cc_start: 0.9392 (mtm) cc_final: 0.8941 (mtm) REVERT: B 227 MET cc_start: 0.9160 (mtp) cc_final: 0.8919 (mtp) REVERT: B 256 ARG cc_start: 0.8451 (tmt170) cc_final: 0.8235 (tpt90) REVERT: B 286 ASP cc_start: 0.8401 (m-30) cc_final: 0.8119 (m-30) REVERT: B 307 TYR cc_start: 0.9135 (t80) cc_final: 0.8529 (t80) REVERT: B 348 MET cc_start: 0.9046 (ppp) cc_final: 0.8477 (ppp) REVERT: B 349 LEU cc_start: 0.9370 (mt) cc_final: 0.8934 (mt) REVERT: B 370 ASN cc_start: 0.9291 (m-40) cc_final: 0.8625 (m110) REVERT: B 385 VAL cc_start: 0.8931 (t) cc_final: 0.8713 (t) REVERT: B 402 GLU cc_start: 0.7954 (mp0) cc_final: 0.7516 (mp0) REVERT: B 475 ASN cc_start: 0.9043 (m110) cc_final: 0.8741 (m110) REVERT: B 515 ASP cc_start: 0.8910 (m-30) cc_final: 0.8449 (p0) REVERT: B 546 LEU cc_start: 0.9448 (mm) cc_final: 0.9119 (mp) REVERT: B 558 TRP cc_start: 0.8745 (m100) cc_final: 0.8354 (m100) REVERT: B 574 TYR cc_start: 0.8250 (m-80) cc_final: 0.7894 (m-80) REVERT: B 586 TYR cc_start: 0.8961 (m-80) cc_final: 0.8562 (m-80) REVERT: B 623 TRP cc_start: 0.8406 (t-100) cc_final: 0.8112 (t-100) REVERT: B 656 LEU cc_start: 0.9285 (mt) cc_final: 0.9009 (mt) REVERT: C 21 PHE cc_start: 0.9001 (m-80) cc_final: 0.8505 (m-80) REVERT: C 23 ASN cc_start: 0.9711 (m-40) cc_final: 0.9463 (m-40) REVERT: C 56 MET cc_start: 0.0944 (ptm) cc_final: 0.0555 (ttp) REVERT: C 74 MET cc_start: 0.9392 (mpp) cc_final: 0.9063 (mpp) REVERT: C 150 GLU cc_start: 0.7937 (tt0) cc_final: 0.7641 (tt0) REVERT: C 154 PHE cc_start: 0.9214 (t80) cc_final: 0.8761 (t80) REVERT: C 157 MET cc_start: 0.9355 (mtm) cc_final: 0.8902 (ptt) REVERT: C 163 LEU cc_start: 0.9093 (tt) cc_final: 0.8768 (tp) REVERT: C 174 TYR cc_start: 0.8858 (t80) cc_final: 0.7660 (t80) REVERT: C 212 ILE cc_start: 0.8408 (OUTLIER) cc_final: 0.7672 (mm) REVERT: C 226 GLU cc_start: 0.8703 (tt0) cc_final: 0.8450 (tt0) REVERT: C 231 LEU cc_start: 0.8843 (tp) cc_final: 0.8517 (tp) REVERT: C 285 ILE cc_start: 0.6650 (tp) cc_final: 0.6227 (tp) REVERT: D 16 ASP cc_start: 0.6751 (t0) cc_final: 0.6465 (t0) REVERT: D 109 PHE cc_start: 0.8695 (m-10) cc_final: 0.8490 (m-80) REVERT: D 115 THR cc_start: 0.8491 (m) cc_final: 0.8262 (p) REVERT: D 119 ASN cc_start: 0.8479 (m110) cc_final: 0.8140 (m-40) REVERT: D 128 ASN cc_start: 0.8950 (t0) cc_final: 0.8068 (t0) REVERT: D 133 LYS cc_start: 0.8134 (ttmt) cc_final: 0.7832 (tptp) REVERT: E 25 TRP cc_start: 0.8192 (p-90) cc_final: 0.7764 (p-90) REVERT: E 46 MET cc_start: 0.8177 (tpp) cc_final: 0.7011 (mpp) REVERT: E 70 MET cc_start: 0.8126 (mmp) cc_final: 0.7288 (mpp) outliers start: 6 outliers final: 2 residues processed: 742 average time/residue: 0.1144 time to fit residues: 128.2034 Evaluate side-chains 599 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 596 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 10.0000 chunk 138 optimal weight: 2.9990 chunk 156 optimal weight: 7.9990 chunk 130 optimal weight: 10.0000 chunk 97 optimal weight: 0.7980 chunk 47 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 128 optimal weight: 6.9990 chunk 146 optimal weight: 2.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- 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 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 320 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 588 GLN A 645 GLN B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 186 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.132727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.095650 restraints weight = 42760.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.099158 restraints weight = 23311.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.101396 restraints weight = 14800.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.102972 restraints weight = 10620.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103947 restraints weight = 8248.277| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3322 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3322 r_free = 0.3322 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3322 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5163 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= 0.169 Angle : 0.624 13.221 23026 Z= 0.324 Chirality : 0.044 0.278 2464 Planarity : 0.004 0.057 2931 Dihedral : 10.518 149.558 2325 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.19), residues: 2012 helix: 1.29 (0.15), residues: 1157 sheet: -0.13 (0.39), residues: 167 loop : 0.43 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.028 0.002 TYR C 174 PHE 0.037 0.002 PHE D 154 TRP 0.011 0.001 TRP B 558 HIS 0.007 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00368 (17038) covalent geometry : angle 0.62286 (23020) SS BOND : bond 0.01331 ( 3) SS BOND : angle 1.95409 ( 6) hydrogen bonds : bond 0.04325 ( 912) hydrogen bonds : angle 4.89747 ( 2664) *********************** 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 712 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 712 time to evaluate : 0.427 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: A 119 GLU cc_start: 0.8446 (mp0) cc_final: 0.8222 (mm-30) REVERT: A 147 GLN cc_start: 0.8269 (tp-100) cc_final: 0.7604 (mm-40) REVERT: A 223 VAL cc_start: 0.9441 (m) cc_final: 0.9135 (p) REVERT: A 254 PHE cc_start: 0.8767 (m-80) cc_final: 0.8443 (m-80) REVERT: A 286 ASP cc_start: 0.8675 (m-30) cc_final: 0.8424 (m-30) REVERT: A 301 PHE cc_start: 0.8902 (m-80) cc_final: 0.8697 (m-80) REVERT: A 367 VAL cc_start: 0.9580 (m) cc_final: 0.9320 (p) REVERT: A 417 LEU cc_start: 0.9403 (tp) cc_final: 0.9169 (tp) REVERT: A 421 GLU cc_start: 0.8298 (pp20) cc_final: 0.7957 (pp20) REVERT: A 453 ARG cc_start: 0.9272 (ttt-90) cc_final: 0.9055 (ttp80) REVERT: A 475 ASN cc_start: 0.8374 (m110) cc_final: 0.8086 (m110) REVERT: A 498 TYR cc_start: 0.9044 (m-80) cc_final: 0.8696 (m-10) REVERT: A 501 GLN cc_start: 0.8925 (tt0) cc_final: 0.8628 (tt0) REVERT: A 509 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8557 (tm-30) REVERT: A 558 TRP cc_start: 0.8934 (m100) cc_final: 0.8617 (m100) REVERT: A 615 MET cc_start: 0.9021 (mmm) cc_final: 0.8602 (mmm) REVERT: A 639 ASP cc_start: 0.8866 (m-30) cc_final: 0.8648 (m-30) REVERT: A 658 LEU cc_start: 0.9572 (mp) cc_final: 0.9334 (mp) REVERT: A 686 ARG cc_start: 0.8017 (ttm-80) cc_final: 0.7063 (mtp180) REVERT: B 27 ASP cc_start: 0.9454 (p0) cc_final: 0.9058 (p0) REVERT: B 30 LYS cc_start: 0.9088 (tptt) cc_final: 0.8841 (tptp) REVERT: B 99 LYS cc_start: 0.9386 (tptm) cc_final: 0.9033 (tptp) REVERT: B 127 LEU cc_start: 0.9789 (mt) cc_final: 0.9518 (mm) REVERT: B 129 PHE cc_start: 0.9173 (m-80) cc_final: 0.8921 (m-80) REVERT: B 135 GLU cc_start: 0.9027 (mp0) cc_final: 0.8821 (pm20) REVERT: B 147 GLN cc_start: 0.8989 (mt0) cc_final: 0.8577 (mt0) REVERT: B 150 GLN cc_start: 0.9367 (tp40) cc_final: 0.8792 (tp-100) REVERT: B 156 PHE cc_start: 0.9296 (t80) cc_final: 0.9067 (t80) REVERT: B 184 ARG cc_start: 0.9517 (tpp80) cc_final: 0.9183 (tpp80) REVERT: B 232 ASN cc_start: 0.9155 (m-40) cc_final: 0.8941 (m110) REVERT: B 252 ASN cc_start: 0.9390 (t0) cc_final: 0.8987 (t0) REVERT: B 256 ARG cc_start: 0.8382 (tmt170) cc_final: 0.8020 (tpt90) REVERT: B 286 ASP cc_start: 0.8325 (m-30) cc_final: 0.8038 (m-30) REVERT: B 307 TYR cc_start: 0.9166 (t80) cc_final: 0.8793 (t80) REVERT: B 322 MET cc_start: 0.8416 (mmt) cc_final: 0.8186 (mmm) REVERT: B 335 GLU cc_start: 0.7651 (tm-30) cc_final: 0.7305 (tm-30) REVERT: B 348 MET cc_start: 0.8965 (ppp) cc_final: 0.8465 (ppp) REVERT: B 349 LEU cc_start: 0.9366 (mt) cc_final: 0.8856 (mt) REVERT: B 370 ASN cc_start: 0.9542 (m-40) cc_final: 0.9084 (m110) REVERT: B 378 PHE cc_start: 0.8856 (p90) cc_final: 0.8562 (p90) REVERT: B 402 GLU cc_start: 0.8129 (mp0) cc_final: 0.7744 (mp0) REVERT: B 475 ASN cc_start: 0.9000 (m-40) cc_final: 0.8652 (m110) REVERT: B 490 THR cc_start: 0.9278 (m) cc_final: 0.9006 (p) REVERT: B 515 ASP cc_start: 0.8950 (m-30) cc_final: 0.8535 (p0) REVERT: B 526 GLU cc_start: 0.8875 (mp0) cc_final: 0.8615 (mp0) REVERT: B 574 TYR cc_start: 0.8421 (m-80) cc_final: 0.8168 (m-80) REVERT: B 586 TYR cc_start: 0.9025 (m-80) cc_final: 0.8795 (m-80) REVERT: B 612 TYR cc_start: 0.8360 (m-80) cc_final: 0.7859 (m-80) REVERT: B 623 TRP cc_start: 0.8469 (t-100) cc_final: 0.8023 (t-100) REVERT: C 17 PHE cc_start: 0.8957 (p90) cc_final: 0.8281 (p90) REVERT: C 20 MET cc_start: 0.9108 (ppp) cc_final: 0.8870 (ppp) REVERT: C 21 PHE cc_start: 0.8969 (m-80) cc_final: 0.8248 (m-80) REVERT: C 56 MET cc_start: 0.0820 (ptm) cc_final: 0.0549 (ptm) REVERT: C 74 MET cc_start: 0.9401 (mpp) cc_final: 0.9076 (mpp) REVERT: C 89 VAL cc_start: 0.7605 (t) cc_final: 0.7097 (t) REVERT: C 95 MET cc_start: 0.8552 (ttp) cc_final: 0.7955 (ttp) REVERT: C 157 MET cc_start: 0.9425 (mtm) cc_final: 0.9030 (ptp) REVERT: C 163 LEU cc_start: 0.9193 (tt) cc_final: 0.8855 (tp) REVERT: C 174 TYR cc_start: 0.8801 (t80) cc_final: 0.7538 (t80) REVERT: C 178 PHE cc_start: 0.8850 (m-10) cc_final: 0.7986 (m-10) REVERT: C 212 ILE cc_start: 0.8681 (mt) cc_final: 0.8329 (mm) REVERT: C 226 GLU cc_start: 0.8722 (tt0) cc_final: 0.8521 (tt0) REVERT: C 227 PHE cc_start: 0.8820 (t80) cc_final: 0.8558 (t80) REVERT: D 42 LEU cc_start: 0.9262 (mt) cc_final: 0.8824 (mp) REVERT: D 109 PHE cc_start: 0.8729 (m-10) cc_final: 0.8431 (m-80) REVERT: D 115 THR cc_start: 0.8410 (m) cc_final: 0.8088 (p) REVERT: D 119 ASN cc_start: 0.8547 (m110) cc_final: 0.8230 (m-40) REVERT: D 128 ASN cc_start: 0.8382 (t0) cc_final: 0.7333 (t0) REVERT: D 133 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7962 (tptp) REVERT: D 242 TYR cc_start: 0.7946 (t80) cc_final: 0.7553 (t80) REVERT: E 25 TRP cc_start: 0.8228 (p-90) cc_final: 0.7807 (p-90) REVERT: E 46 MET cc_start: 0.8187 (tpp) cc_final: 0.7958 (tpp) REVERT: E 70 MET cc_start: 0.8120 (mmp) cc_final: 0.7289 (mpp) outliers start: 0 outliers final: 0 residues processed: 712 average time/residue: 0.1088 time to fit residues: 117.9392 Evaluate side-chains 584 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 584 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 38 optimal weight: 0.9980 chunk 85 optimal weight: 3.9990 chunk 145 optimal weight: 20.0000 chunk 2 optimal weight: 5.9990 chunk 180 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 80 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 chunk 112 optimal weight: 0.3980 chunk 138 optimal weight: 20.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 147 GLN A 150 GLN A 180 ASN A 304 HIS A 365 ASN A 418 ASN ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 645 GLN B 218 ASN B 232 ASN ** 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 = 0.3817 r_free = 0.3817 target = 0.135647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.097822 restraints weight = 41790.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101514 restraints weight = 21311.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.103976 restraints weight = 13358.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.105681 restraints weight = 9332.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.106741 restraints weight = 7151.654| |-----------------------------------------------------------------------------| r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3354 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3354 r_free = 0.3354 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3354 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.5650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 17041 Z= 0.137 Angle : 0.607 11.464 23026 Z= 0.316 Chirality : 0.044 0.290 2464 Planarity : 0.004 0.038 2931 Dihedral : 10.224 142.676 2325 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.06 % Allowed : 2.12 % Favored : 97.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.06 (0.19), residues: 2012 helix: 1.18 (0.15), residues: 1165 sheet: -0.11 (0.41), residues: 165 loop : 0.29 (0.24), residues: 682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 446 TYR 0.027 0.001 TYR C 169 PHE 0.045 0.002 PHE D 154 TRP 0.007 0.001 TRP A 623 HIS 0.006 0.001 HIS B 438 Details of bonding type rmsd covalent geometry : bond 0.00303 (17038) covalent geometry : angle 0.60381 (23020) SS BOND : bond 0.00307 ( 3) SS BOND : angle 3.79986 ( 6) hydrogen bonds : bond 0.04067 ( 912) hydrogen bonds : angle 4.91293 ( 2664) *********************** 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 709 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 708 time to evaluate : 0.515 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 87 LYS cc_start: 0.8572 (tttp) cc_final: 0.8307 (ttmm) REVERT: A 145 ILE cc_start: 0.9118 (tp) cc_final: 0.8826 (tp) REVERT: A 162 LYS cc_start: 0.9398 (tmtt) cc_final: 0.8913 (tmmt) REVERT: A 234 PHE cc_start: 0.9418 (m-80) cc_final: 0.9134 (m-80) REVERT: A 250 TYR cc_start: 0.8100 (m-80) cc_final: 0.7659 (m-80) REVERT: A 360 PHE cc_start: 0.8689 (m-80) cc_final: 0.8390 (m-80) REVERT: A 367 VAL cc_start: 0.9557 (m) cc_final: 0.9294 (p) REVERT: A 390 GLN cc_start: 0.8595 (mt0) cc_final: 0.8238 (mt0) REVERT: A 417 LEU cc_start: 0.9447 (tp) cc_final: 0.9101 (tp) REVERT: A 421 GLU cc_start: 0.8411 (pp20) cc_final: 0.8021 (pp20) REVERT: A 475 ASN cc_start: 0.8235 (m110) cc_final: 0.8015 (m-40) REVERT: A 509 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8490 (tm-30) REVERT: A 515 ASP cc_start: 0.8828 (m-30) cc_final: 0.8579 (m-30) REVERT: A 615 MET cc_start: 0.9040 (mmm) cc_final: 0.8623 (mmm) REVERT: A 658 LEU cc_start: 0.9566 (mp) cc_final: 0.9105 (mp) REVERT: A 686 ARG cc_start: 0.7948 (ttm-80) cc_final: 0.7150 (mtp180) REVERT: B 30 LYS cc_start: 0.9128 (tptt) cc_final: 0.8870 (tptt) REVERT: B 87 LYS cc_start: 0.9044 (tppt) cc_final: 0.8409 (ttmt) REVERT: B 99 LYS cc_start: 0.9429 (tptm) cc_final: 0.9062 (tptp) REVERT: B 127 LEU cc_start: 0.9801 (mt) cc_final: 0.9472 (mm) REVERT: B 129 PHE cc_start: 0.9154 (m-80) cc_final: 0.8880 (m-80) REVERT: B 135 GLU cc_start: 0.8986 (mp0) cc_final: 0.8768 (pm20) REVERT: B 145 ILE cc_start: 0.9322 (tp) cc_final: 0.8985 (tp) REVERT: B 147 GLN cc_start: 0.8922 (mt0) cc_final: 0.8499 (mt0) REVERT: B 150 GLN cc_start: 0.9510 (tp40) cc_final: 0.9006 (tp-100) REVERT: B 190 MET cc_start: 0.9329 (mtm) cc_final: 0.9015 (mtm) REVERT: B 217 GLU cc_start: 0.9269 (tm-30) cc_final: 0.9047 (tm-30) REVERT: B 218 ASN cc_start: 0.8688 (OUTLIER) cc_final: 0.8430 (t0) REVERT: B 252 ASN cc_start: 0.9355 (t0) cc_final: 0.9027 (t0) REVERT: B 256 ARG cc_start: 0.8359 (tmt170) cc_final: 0.8043 (ttp80) REVERT: B 286 ASP cc_start: 0.8408 (m-30) cc_final: 0.8043 (m-30) REVERT: B 322 MET cc_start: 0.8466 (mmt) cc_final: 0.8237 (mmm) REVERT: B 348 MET cc_start: 0.8962 (ppp) cc_final: 0.8458 (ppp) REVERT: B 349 LEU cc_start: 0.9346 (mt) cc_final: 0.8648 (mt) REVERT: B 370 ASN cc_start: 0.9456 (m-40) cc_final: 0.9064 (m110) REVERT: B 378 PHE cc_start: 0.8935 (p90) cc_final: 0.8564 (p90) REVERT: B 402 GLU cc_start: 0.8109 (mp0) cc_final: 0.7722 (mp0) REVERT: B 415 ASN cc_start: 0.9053 (t0) cc_final: 0.8842 (t0) REVERT: B 437 THR cc_start: 0.9581 (m) cc_final: 0.9257 (m) REVERT: B 446 ARG cc_start: 0.7382 (mmt-90) cc_final: 0.7160 (mmt-90) REVERT: B 475 ASN cc_start: 0.9133 (m-40) cc_final: 0.8840 (m110) REVERT: B 493 MET cc_start: 0.9340 (tmm) cc_final: 0.8649 (tmm) REVERT: B 515 ASP cc_start: 0.8891 (m-30) cc_final: 0.8510 (p0) REVERT: B 526 GLU cc_start: 0.8826 (mp0) cc_final: 0.8560 (mp0) REVERT: B 550 MET cc_start: 0.8128 (mtp) cc_final: 0.7712 (mtp) REVERT: B 574 TYR cc_start: 0.8416 (m-80) cc_final: 0.8012 (m-80) REVERT: B 612 TYR cc_start: 0.8179 (m-80) cc_final: 0.7754 (m-80) REVERT: B 656 LEU cc_start: 0.9230 (mt) cc_final: 0.9007 (mt) REVERT: C 17 PHE cc_start: 0.8906 (p90) cc_final: 0.8231 (p90) REVERT: C 20 MET cc_start: 0.9188 (ppp) cc_final: 0.8907 (ppp) REVERT: C 21 PHE cc_start: 0.9018 (m-80) cc_final: 0.8391 (m-80) REVERT: C 46 TYR cc_start: 0.7674 (m-80) cc_final: 0.7363 (m-80) REVERT: C 74 MET cc_start: 0.9373 (mpp) cc_final: 0.9052 (mpp) REVERT: C 87 LYS cc_start: 0.8903 (ptpp) cc_final: 0.8691 (ptpp) REVERT: C 89 VAL cc_start: 0.7529 (t) cc_final: 0.6820 (t) REVERT: C 95 MET cc_start: 0.8544 (ttp) cc_final: 0.7929 (ttp) REVERT: C 163 LEU cc_start: 0.9192 (tt) cc_final: 0.8927 (tp) REVERT: C 174 TYR cc_start: 0.8790 (t80) cc_final: 0.7947 (t80) REVERT: C 226 GLU cc_start: 0.8829 (tt0) cc_final: 0.8567 (tt0) REVERT: C 274 ASP cc_start: 0.8780 (p0) cc_final: 0.8456 (p0) REVERT: D 42 LEU cc_start: 0.9302 (mt) cc_final: 0.9065 (mp) REVERT: D 109 PHE cc_start: 0.8688 (m-10) cc_final: 0.8348 (m-80) REVERT: D 115 THR cc_start: 0.8367 (m) cc_final: 0.8122 (p) REVERT: D 119 ASN cc_start: 0.8548 (m110) cc_final: 0.8306 (m-40) REVERT: D 128 ASN cc_start: 0.8370 (t0) cc_final: 0.7274 (t0) REVERT: D 133 LYS cc_start: 0.8465 (ttmt) cc_final: 0.8080 (tptp) REVERT: D 242 TYR cc_start: 0.7966 (t80) cc_final: 0.7515 (t80) REVERT: E 25 TRP cc_start: 0.8264 (p-90) cc_final: 0.7608 (p-90) REVERT: E 46 MET cc_start: 0.8234 (tpp) cc_final: 0.7972 (tpp) REVERT: E 67 TYR cc_start: 0.8579 (m-80) cc_final: 0.8357 (m-10) REVERT: E 70 MET cc_start: 0.8097 (mmp) cc_final: 0.7837 (mpp) outliers start: 1 outliers final: 0 residues processed: 708 average time/residue: 0.1192 time to fit residues: 127.8805 Evaluate side-chains 576 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 575 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 56 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 65 optimal weight: 8.9990 chunk 146 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 104 optimal weight: 0.7980 chunk 172 optimal weight: 3.9990 chunk 138 optimal weight: 30.0000 chunk 134 optimal weight: 9.9990 chunk 21 optimal weight: 0.0170 chunk 90 optimal weight: 3.9990 overall best weight: 2.5624 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 91 ASN C 238 ASN C 270 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.096117 restraints weight = 43228.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.099364 restraints weight = 22808.636| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.101528 restraints weight = 14622.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.103041 restraints weight = 10401.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.104103 restraints weight = 8176.860| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3260 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3260 r_free = 0.3260 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3260 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 17041 Z= 0.212 Angle : 0.661 11.285 23026 Z= 0.342 Chirality : 0.045 0.328 2464 Planarity : 0.004 0.077 2931 Dihedral : 10.375 146.871 2325 Min Nonbonded Distance : 1.764 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.06 % Allowed : 2.01 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.98 (0.19), residues: 2012 helix: 1.08 (0.15), residues: 1151 sheet: -0.14 (0.40), residues: 167 loop : 0.34 (0.24), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.001 ARG D 225 TYR 0.032 0.002 TYR C 174 PHE 0.031 0.002 PHE D 154 TRP 0.019 0.002 TRP A 623 HIS 0.010 0.002 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00462 (17038) covalent geometry : angle 0.65789 (23020) SS BOND : bond 0.00283 ( 3) SS BOND : angle 4.18777 ( 6) hydrogen bonds : bond 0.04092 ( 912) hydrogen bonds : angle 5.10225 ( 2664) *********************** 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 678 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 677 time to evaluate : 0.499 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 45 THR cc_start: 0.9186 (t) cc_final: 0.8838 (t) REVERT: A 117 ARG cc_start: 0.8733 (mtt-85) cc_final: 0.8465 (mtp85) REVERT: A 162 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8971 (ttpt) REVERT: A 228 LYS cc_start: 0.8960 (tptt) cc_final: 0.8596 (mptt) REVERT: A 250 TYR cc_start: 0.8079 (m-80) cc_final: 0.7737 (m-80) REVERT: A 286 ASP cc_start: 0.8758 (m-30) cc_final: 0.8519 (m-30) REVERT: A 301 PHE cc_start: 0.8796 (m-80) cc_final: 0.8328 (m-80) REVERT: A 322 MET cc_start: 0.7897 (mmm) cc_final: 0.7562 (mmm) REVERT: A 367 VAL cc_start: 0.9581 (m) cc_final: 0.9343 (p) REVERT: A 390 GLN cc_start: 0.8729 (mt0) cc_final: 0.8370 (mt0) REVERT: A 421 GLU cc_start: 0.8515 (pp20) cc_final: 0.8220 (pp20) REVERT: A 475 ASN cc_start: 0.8286 (m110) cc_final: 0.8043 (m-40) REVERT: A 498 TYR cc_start: 0.8636 (m-80) cc_final: 0.8177 (m-80) REVERT: A 501 GLN cc_start: 0.9074 (tt0) cc_final: 0.8775 (tt0) REVERT: A 509 GLU cc_start: 0.8872 (tm-30) cc_final: 0.8501 (tm-30) REVERT: A 515 ASP cc_start: 0.8871 (m-30) cc_final: 0.8469 (m-30) REVERT: A 615 MET cc_start: 0.9030 (mmm) cc_final: 0.8648 (mmm) REVERT: A 645 GLN cc_start: 0.8645 (tp40) cc_final: 0.8010 (tp40) REVERT: A 655 THR cc_start: 0.9126 (m) cc_final: 0.8632 (t) REVERT: A 686 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7642 (mtp-110) REVERT: B 18 ILE cc_start: 0.9437 (mm) cc_final: 0.8773 (mm) REVERT: B 40 TYR cc_start: 0.9293 (t80) cc_final: 0.8992 (t80) REVERT: B 87 LYS cc_start: 0.9132 (tppt) cc_final: 0.8608 (ttmt) REVERT: B 117 ARG cc_start: 0.8202 (mmm160) cc_final: 0.7757 (mmm-85) REVERT: B 120 ASP cc_start: 0.8666 (m-30) cc_final: 0.8177 (m-30) REVERT: B 127 LEU cc_start: 0.9794 (mt) cc_final: 0.9503 (mm) REVERT: B 129 PHE cc_start: 0.9086 (m-10) cc_final: 0.8854 (m-80) REVERT: B 145 ILE cc_start: 0.9335 (tp) cc_final: 0.8993 (tp) REVERT: B 147 GLN cc_start: 0.9209 (mt0) cc_final: 0.8251 (mt0) REVERT: B 150 GLN cc_start: 0.9573 (tp40) cc_final: 0.9097 (tp-100) REVERT: B 184 ARG cc_start: 0.9471 (tpp80) cc_final: 0.8611 (tpp80) REVERT: B 186 ILE cc_start: 0.9566 (mt) cc_final: 0.9355 (mt) REVERT: B 190 MET cc_start: 0.9228 (mtm) cc_final: 0.9025 (mtm) REVERT: B 231 ASP cc_start: 0.8425 (t70) cc_final: 0.7307 (t70) REVERT: B 232 ASN cc_start: 0.9076 (m110) cc_final: 0.8715 (m110) REVERT: B 235 ARG cc_start: 0.8746 (mtm-85) cc_final: 0.7874 (mtm-85) REVERT: B 256 ARG cc_start: 0.8250 (tmt170) cc_final: 0.7955 (ttp80) REVERT: B 258 ILE cc_start: 0.9410 (tp) cc_final: 0.9187 (tp) REVERT: B 286 ASP cc_start: 0.8428 (m-30) cc_final: 0.8216 (m-30) REVERT: B 335 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7467 (tm-30) REVERT: B 348 MET cc_start: 0.8947 (ppp) cc_final: 0.8450 (ppp) REVERT: B 349 LEU cc_start: 0.9355 (mt) cc_final: 0.8585 (mt) REVERT: B 361 GLN cc_start: 0.8385 (tm-30) cc_final: 0.8015 (tp40) REVERT: B 370 ASN cc_start: 0.9511 (m-40) cc_final: 0.9164 (m110) REVERT: B 378 PHE cc_start: 0.9007 (p90) cc_final: 0.8663 (p90) REVERT: B 402 GLU cc_start: 0.8182 (mp0) cc_final: 0.7536 (mp0) REVERT: B 416 ILE cc_start: 0.8862 (mm) cc_final: 0.8637 (mm) REVERT: B 437 THR cc_start: 0.9591 (m) cc_final: 0.9219 (m) REVERT: B 475 ASN cc_start: 0.9145 (m-40) cc_final: 0.8859 (m110) REVERT: B 490 THR cc_start: 0.9282 (m) cc_final: 0.8949 (p) REVERT: B 493 MET cc_start: 0.9281 (tmm) cc_final: 0.8625 (tmm) REVERT: B 515 ASP cc_start: 0.8890 (m-30) cc_final: 0.8653 (p0) REVERT: B 526 GLU cc_start: 0.8871 (mp0) cc_final: 0.8594 (mp0) REVERT: B 550 MET cc_start: 0.8109 (mtp) cc_final: 0.7819 (mtp) REVERT: B 612 TYR cc_start: 0.8068 (m-80) cc_final: 0.7604 (m-80) REVERT: B 623 TRP cc_start: 0.8331 (t-100) cc_final: 0.7533 (t-100) REVERT: B 632 MET cc_start: 0.7464 (mtm) cc_final: 0.7162 (mtp) REVERT: B 656 LEU cc_start: 0.9315 (mt) cc_final: 0.9054 (mt) REVERT: C 17 PHE cc_start: 0.8983 (p90) cc_final: 0.8310 (p90) REVERT: C 20 MET cc_start: 0.9230 (ppp) cc_final: 0.8930 (ppp) REVERT: C 21 PHE cc_start: 0.9040 (m-80) cc_final: 0.8477 (m-80) REVERT: C 74 MET cc_start: 0.9287 (mpp) cc_final: 0.8954 (mpp) REVERT: C 95 MET cc_start: 0.8470 (ttp) cc_final: 0.7701 (ttp) REVERT: C 174 TYR cc_start: 0.8903 (t80) cc_final: 0.8335 (t80) REVERT: C 226 GLU cc_start: 0.8887 (tt0) cc_final: 0.8642 (tt0) REVERT: C 231 LEU cc_start: 0.9105 (mt) cc_final: 0.8841 (mt) REVERT: C 274 ASP cc_start: 0.8645 (p0) cc_final: 0.8232 (p0) REVERT: D 109 PHE cc_start: 0.8740 (m-10) cc_final: 0.8435 (m-80) REVERT: D 128 ASN cc_start: 0.8372 (t0) cc_final: 0.7780 (t0) REVERT: D 185 MET cc_start: 0.7044 (ptm) cc_final: 0.6804 (ptm) REVERT: E 25 TRP cc_start: 0.8341 (p-90) cc_final: 0.7628 (p-90) REVERT: E 46 MET cc_start: 0.8342 (tpp) cc_final: 0.8085 (tpp) REVERT: E 60 ASN cc_start: 0.9367 (t0) cc_final: 0.9106 (t0) outliers start: 1 outliers final: 0 residues processed: 678 average time/residue: 0.1081 time to fit residues: 113.0763 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 : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 191 optimal weight: 1.9990 chunk 60 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 18 optimal weight: 0.5980 chunk 124 optimal weight: 0.3980 chunk 109 optimal weight: 2.9990 chunk 153 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 195 optimal weight: 1.9990 chunk 104 optimal weight: 1.9990 chunk 175 optimal weight: 20.0000 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 34 HIS ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN C 270 ASN ** D 91 ASN ** 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 = 0.3788 r_free = 0.3788 target = 0.134296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.096030 restraints weight = 42464.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.099745 restraints weight = 21520.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.102122 restraints weight = 13267.747| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3309 r_free = 0.3309 target = 0.103616 restraints weight = 9362.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.104690 restraints weight = 7304.357| |-----------------------------------------------------------------------------| r_work (final): 0.3302 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3309 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3309 r_free = 0.3309 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 = 0.3309 r_free = 0.3309 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3309 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7499 moved from start: 0.6441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.092 17041 Z= 0.157 Angle : 0.638 12.140 23026 Z= 0.328 Chirality : 0.044 0.268 2464 Planarity : 0.004 0.051 2931 Dihedral : 10.261 145.017 2325 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 13.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.11 % Allowed : 1.79 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.88 (0.19), residues: 2012 helix: 1.04 (0.15), residues: 1154 sheet: -0.22 (0.40), residues: 167 loop : 0.23 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 225 TYR 0.044 0.002 TYR B 574 PHE 0.034 0.002 PHE A 234 TRP 0.012 0.001 TRP A 623 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00351 (17038) covalent geometry : angle 0.63206 (23020) SS BOND : bond 0.00627 ( 3) SS BOND : angle 5.39375 ( 6) hydrogen bonds : bond 0.03884 ( 912) hydrogen bonds : angle 5.02973 ( 2664) *********************** 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 673 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 671 time to evaluate : 0.558 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: A 8 LYS cc_start: 0.8921 (tptp) cc_final: 0.8592 (tppt) REVERT: A 113 LYS cc_start: 0.9518 (mmtt) cc_final: 0.9225 (mmmm) REVERT: A 145 ILE cc_start: 0.9110 (tp) cc_final: 0.8877 (tp) REVERT: A 147 GLN cc_start: 0.8649 (tp-100) cc_final: 0.8016 (tp-100) REVERT: A 162 LYS cc_start: 0.9277 (tmtt) cc_final: 0.9005 (ttpt) REVERT: A 187 ASP cc_start: 0.8770 (t70) cc_final: 0.8413 (t0) REVERT: A 209 LYS cc_start: 0.9307 (tttm) cc_final: 0.9101 (tttm) REVERT: A 228 LYS cc_start: 0.9069 (tptt) cc_final: 0.8672 (mptt) REVERT: A 230 LEU cc_start: 0.9754 (mt) cc_final: 0.9532 (mt) REVERT: A 234 PHE cc_start: 0.9472 (m-80) cc_final: 0.9238 (m-80) REVERT: A 250 TYR cc_start: 0.8192 (m-80) cc_final: 0.7829 (m-80) REVERT: A 254 PHE cc_start: 0.8748 (m-80) cc_final: 0.8268 (m-80) REVERT: A 257 ASP cc_start: 0.9035 (m-30) cc_final: 0.8741 (m-30) REVERT: A 301 PHE cc_start: 0.8893 (m-80) cc_final: 0.8511 (m-80) REVERT: A 338 ASN cc_start: 0.9497 (t0) cc_final: 0.9085 (t0) REVERT: A 348 MET cc_start: 0.8892 (ptm) cc_final: 0.8683 (ptm) REVERT: A 367 VAL cc_start: 0.9586 (m) cc_final: 0.9352 (p) REVERT: A 390 GLN cc_start: 0.8703 (mt0) cc_final: 0.8391 (mt0) REVERT: A 421 GLU cc_start: 0.8609 (pp20) cc_final: 0.8306 (pp20) REVERT: A 498 TYR cc_start: 0.8675 (m-80) cc_final: 0.8316 (m-80) REVERT: A 501 GLN cc_start: 0.9042 (tt0) cc_final: 0.8533 (tm-30) REVERT: A 509 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8558 (tm-30) REVERT: A 515 ASP cc_start: 0.8878 (m-30) cc_final: 0.8437 (m-30) REVERT: A 558 TRP cc_start: 0.9043 (m100) cc_final: 0.8695 (m100) REVERT: A 590 SER cc_start: 0.9413 (p) cc_final: 0.9143 (t) REVERT: A 615 MET cc_start: 0.8983 (mmm) cc_final: 0.8622 (mmm) REVERT: A 645 GLN cc_start: 0.8600 (tp40) cc_final: 0.8138 (tp-100) REVERT: A 655 THR cc_start: 0.9020 (m) cc_final: 0.8538 (t) REVERT: A 686 ARG cc_start: 0.8220 (ttm-80) cc_final: 0.7686 (mtp-110) REVERT: B 16 ILE cc_start: 0.9121 (tp) cc_final: 0.8813 (tp) REVERT: B 18 ILE cc_start: 0.9464 (mm) cc_final: 0.9186 (tp) REVERT: B 30 LYS cc_start: 0.9094 (tptt) cc_final: 0.8882 (tptt) REVERT: B 40 TYR cc_start: 0.9339 (t80) cc_final: 0.9004 (t80) REVERT: B 87 LYS cc_start: 0.9136 (tppt) cc_final: 0.8589 (ttmt) REVERT: B 117 ARG cc_start: 0.8223 (mmm160) cc_final: 0.7760 (mmm-85) REVERT: B 120 ASP cc_start: 0.8672 (m-30) cc_final: 0.8255 (m-30) REVERT: B 127 LEU cc_start: 0.9774 (mt) cc_final: 0.9477 (mm) REVERT: B 129 PHE cc_start: 0.9164 (m-10) cc_final: 0.8872 (m-80) REVERT: B 145 ILE cc_start: 0.9351 (tp) cc_final: 0.9001 (tp) REVERT: B 147 GLN cc_start: 0.9171 (mt0) cc_final: 0.8201 (mt0) REVERT: B 184 ARG cc_start: 0.9482 (tpp80) cc_final: 0.8505 (tpp80) REVERT: B 231 ASP cc_start: 0.8497 (t70) cc_final: 0.7462 (t70) REVERT: B 235 ARG cc_start: 0.8766 (mtm-85) cc_final: 0.8051 (mtm-85) REVERT: B 256 ARG cc_start: 0.8289 (tmt170) cc_final: 0.8029 (ttp80) REVERT: B 258 ILE cc_start: 0.9376 (tp) cc_final: 0.9129 (tp) REVERT: B 314 MET cc_start: 0.9120 (ppp) cc_final: 0.8884 (ppp) REVERT: B 348 MET cc_start: 0.8958 (ppp) cc_final: 0.8396 (ppp) REVERT: B 349 LEU cc_start: 0.9358 (mt) cc_final: 0.8645 (mt) REVERT: B 375 LYS cc_start: 0.8923 (mmmm) cc_final: 0.8404 (mmmm) REVERT: B 378 PHE cc_start: 0.9001 (p90) cc_final: 0.8645 (p90) REVERT: B 402 GLU cc_start: 0.8220 (mp0) cc_final: 0.7521 (mp0) REVERT: B 437 THR cc_start: 0.9540 (m) cc_final: 0.9224 (m) REVERT: B 446 ARG cc_start: 0.7555 (mpt90) cc_final: 0.7016 (mpt90) REVERT: B 475 ASN cc_start: 0.9145 (m-40) cc_final: 0.8933 (m110) REVERT: B 490 THR cc_start: 0.9271 (m) cc_final: 0.8889 (p) REVERT: B 493 MET cc_start: 0.9279 (tmm) cc_final: 0.8623 (tmm) REVERT: B 515 ASP cc_start: 0.8920 (m-30) cc_final: 0.8537 (p0) REVERT: B 526 GLU cc_start: 0.8855 (mp0) cc_final: 0.8634 (mp0) REVERT: B 550 MET cc_start: 0.8112 (mtp) cc_final: 0.7827 (mtp) REVERT: B 612 TYR cc_start: 0.8473 (m-80) cc_final: 0.8088 (m-80) REVERT: B 623 TRP cc_start: 0.8417 (t-100) cc_final: 0.8102 (t-100) REVERT: B 656 LEU cc_start: 0.9247 (mt) cc_final: 0.9047 (mt) REVERT: C 17 PHE cc_start: 0.9045 (p90) cc_final: 0.8355 (p90) REVERT: C 20 MET cc_start: 0.9273 (ppp) cc_final: 0.9007 (ppp) REVERT: C 21 PHE cc_start: 0.9052 (m-80) cc_final: 0.8500 (m-80) REVERT: C 46 TYR cc_start: 0.7910 (m-10) cc_final: 0.7692 (m-80) REVERT: C 68 GLU cc_start: 0.8976 (mp0) cc_final: 0.8704 (pm20) REVERT: C 74 MET cc_start: 0.9219 (mpp) cc_final: 0.8926 (mpp) REVERT: C 89 VAL cc_start: 0.7641 (t) cc_final: 0.7023 (t) REVERT: C 95 MET cc_start: 0.8473 (ttp) cc_final: 0.7813 (ttp) REVERT: C 174 TYR cc_start: 0.8921 (t80) cc_final: 0.7606 (t80) REVERT: C 178 PHE cc_start: 0.8942 (m-10) cc_final: 0.8607 (m-10) REVERT: C 226 GLU cc_start: 0.8879 (tt0) cc_final: 0.8646 (tt0) REVERT: C 231 LEU cc_start: 0.9159 (mt) cc_final: 0.8805 (mt) REVERT: C 274 ASP cc_start: 0.8759 (p0) cc_final: 0.8364 (p0) REVERT: D 92 PHE cc_start: 0.6859 (t80) cc_final: 0.6490 (t80) REVERT: D 109 PHE cc_start: 0.8708 (m-10) cc_final: 0.8391 (m-80) REVERT: D 154 PHE cc_start: 0.7421 (m-80) cc_final: 0.6516 (m-80) REVERT: E 24 PHE cc_start: 0.8823 (m-80) cc_final: 0.8549 (m-80) REVERT: E 25 TRP cc_start: 0.8211 (p-90) cc_final: 0.7537 (p-90) REVERT: E 41 GLU cc_start: 0.8775 (pt0) cc_final: 0.8532 (tm-30) REVERT: E 46 MET cc_start: 0.8348 (tpp) cc_final: 0.8047 (tpp) REVERT: E 60 ASN cc_start: 0.9361 (t0) cc_final: 0.9102 (t0) REVERT: E 67 TYR cc_start: 0.8803 (m-10) cc_final: 0.8578 (m-80) REVERT: E 70 MET cc_start: 0.8103 (mmp) cc_final: 0.7498 (mpp) REVERT: E 93 LYS cc_start: 0.7686 (tptp) cc_final: 0.6793 (tptt) outliers start: 2 outliers final: 2 residues processed: 673 average time/residue: 0.1142 time to fit residues: 117.1017 Evaluate side-chains 570 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 568 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 193 optimal weight: 4.9990 chunk 64 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 165 optimal weight: 20.0000 chunk 175 optimal weight: 20.0000 chunk 13 optimal weight: 6.9990 chunk 24 optimal weight: 7.9990 chunk 77 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 117 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 387 GLN ** 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 418 ASN ** B 438 HIS ** 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 234 GLN ** 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.135955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.099164 restraints weight = 42841.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 20)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.102522 restraints weight = 22661.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.104681 restraints weight = 14497.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.106166 restraints weight = 10283.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.107103 restraints weight = 8067.943| |-----------------------------------------------------------------------------| r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3348 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3348 r_free = 0.3348 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3347 r_free = 0.3347 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3347 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.6765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 17041 Z= 0.139 Angle : 0.631 12.207 23026 Z= 0.326 Chirality : 0.044 0.197 2464 Planarity : 0.004 0.042 2931 Dihedral : 10.087 142.565 2325 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.89 (0.19), residues: 2012 helix: 1.09 (0.15), residues: 1144 sheet: -0.24 (0.39), residues: 169 loop : 0.18 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 485 TYR 0.025 0.002 TYR D 105 PHE 0.027 0.002 PHE A 234 TRP 0.010 0.001 TRP A 623 HIS 0.012 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00309 (17038) covalent geometry : angle 0.62650 (23020) SS BOND : bond 0.00592 ( 3) SS BOND : angle 4.43881 ( 6) hydrogen bonds : bond 0.03779 ( 912) hydrogen bonds : angle 5.01335 ( 2664) *********************** 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 672 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 672 time to evaluate : 0.579 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: 0.8942 (tptp) cc_final: 0.8613 (tppt) REVERT: A 147 GLN cc_start: 0.8525 (tp-100) cc_final: 0.7789 (tp-100) REVERT: A 157 LEU cc_start: 0.9104 (tp) cc_final: 0.8802 (tp) REVERT: A 162 LYS cc_start: 0.9243 (tmtt) cc_final: 0.8996 (ttpt) REVERT: A 187 ASP cc_start: 0.8730 (t70) cc_final: 0.8358 (t0) REVERT: A 228 LYS cc_start: 0.9102 (tptt) cc_final: 0.8693 (mptt) REVERT: A 230 LEU cc_start: 0.9741 (mt) cc_final: 0.9514 (mt) REVERT: A 234 PHE cc_start: 0.9400 (m-80) cc_final: 0.9116 (m-80) REVERT: A 250 TYR cc_start: 0.8174 (m-80) cc_final: 0.7797 (m-80) REVERT: A 254 PHE cc_start: 0.8678 (m-80) cc_final: 0.8340 (m-80) REVERT: A 257 ASP cc_start: 0.8982 (m-30) cc_final: 0.8780 (m-30) REVERT: A 261 PHE cc_start: 0.9376 (t80) cc_final: 0.9050 (t80) REVERT: A 262 LEU cc_start: 0.9564 (mt) cc_final: 0.9199 (mt) REVERT: A 286 ASP cc_start: 0.8809 (m-30) cc_final: 0.8598 (m-30) REVERT: A 301 PHE cc_start: 0.8939 (m-80) cc_final: 0.8608 (m-80) REVERT: A 338 ASN cc_start: 0.9380 (t0) cc_final: 0.8260 (t0) REVERT: A 367 VAL cc_start: 0.9601 (m) cc_final: 0.9374 (p) REVERT: A 390 GLN cc_start: 0.8757 (mt0) cc_final: 0.8352 (mt0) REVERT: A 421 GLU cc_start: 0.8667 (pp20) cc_final: 0.8271 (pp20) REVERT: A 498 TYR cc_start: 0.8759 (m-80) cc_final: 0.8340 (m-80) REVERT: A 509 GLU cc_start: 0.8961 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 515 ASP cc_start: 0.8914 (m-30) cc_final: 0.8484 (m-30) REVERT: A 558 TRP cc_start: 0.9043 (m100) cc_final: 0.8665 (m100) REVERT: A 570 MET cc_start: 0.8412 (ptm) cc_final: 0.8080 (ptm) REVERT: A 615 MET cc_start: 0.8955 (mmm) cc_final: 0.8660 (mmm) REVERT: A 645 GLN cc_start: 0.8657 (tp40) cc_final: 0.8163 (tp-100) REVERT: A 686 ARG cc_start: 0.8162 (ttm-80) cc_final: 0.7729 (mtp-110) REVERT: B 18 ILE cc_start: 0.9407 (mm) cc_final: 0.8872 (mm) REVERT: B 40 TYR cc_start: 0.9316 (t80) cc_final: 0.9000 (t80) REVERT: B 87 LYS cc_start: 0.9116 (tppt) cc_final: 0.8479 (ttmt) REVERT: B 112 LYS cc_start: 0.9392 (mmpt) cc_final: 0.9182 (mmmt) REVERT: B 117 ARG cc_start: 0.8443 (mmm160) cc_final: 0.7764 (mmm-85) REVERT: B 120 ASP cc_start: 0.8744 (m-30) cc_final: 0.8345 (m-30) REVERT: B 127 LEU cc_start: 0.9758 (mt) cc_final: 0.9464 (mm) REVERT: B 129 PHE cc_start: 0.9143 (m-10) cc_final: 0.8850 (m-80) REVERT: B 138 LYS cc_start: 0.9467 (mtpt) cc_final: 0.9098 (mttt) REVERT: B 145 ILE cc_start: 0.9380 (tp) cc_final: 0.8987 (tp) REVERT: B 147 GLN cc_start: 0.9189 (mt0) cc_final: 0.8153 (mm-40) REVERT: B 150 GLN cc_start: 0.9546 (tp40) cc_final: 0.9272 (tp-100) REVERT: B 184 ARG cc_start: 0.9514 (tpp80) cc_final: 0.8981 (tpp80) REVERT: B 186 ILE cc_start: 0.9543 (mt) cc_final: 0.9286 (mt) REVERT: B 190 MET cc_start: 0.9380 (mtm) cc_final: 0.8760 (mtm) REVERT: B 228 LYS cc_start: 0.9580 (mmmt) cc_final: 0.9210 (mmmt) REVERT: B 231 ASP cc_start: 0.8475 (t70) cc_final: 0.7030 (t70) REVERT: B 232 ASN cc_start: 0.9098 (m110) cc_final: 0.8686 (m110) REVERT: B 235 ARG cc_start: 0.8846 (mtm-85) cc_final: 0.8023 (mtm-85) REVERT: B 256 ARG cc_start: 0.8259 (tmt170) cc_final: 0.7992 (ttp80) REVERT: B 258 ILE cc_start: 0.9432 (tp) cc_final: 0.9151 (tp) REVERT: B 286 ASP cc_start: 0.8531 (m-30) cc_final: 0.8050 (m-30) REVERT: B 335 GLU cc_start: 0.7842 (tm-30) cc_final: 0.7564 (tm-30) REVERT: B 348 MET cc_start: 0.8991 (ppp) cc_final: 0.8418 (ppp) REVERT: B 349 LEU cc_start: 0.9316 (mt) cc_final: 0.8648 (mt) REVERT: B 361 GLN cc_start: 0.8094 (tm-30) cc_final: 0.7646 (tm-30) REVERT: B 375 LYS cc_start: 0.8929 (mmmm) cc_final: 0.8435 (mmmm) REVERT: B 378 PHE cc_start: 0.8998 (p90) cc_final: 0.8649 (p90) REVERT: B 394 TYR cc_start: 0.8975 (m-80) cc_final: 0.8736 (m-80) REVERT: B 437 THR cc_start: 0.9470 (m) cc_final: 0.9125 (m) REVERT: B 446 ARG cc_start: 0.7792 (mpt90) cc_final: 0.7506 (mpt90) REVERT: B 475 ASN cc_start: 0.9261 (m-40) cc_final: 0.8989 (m110) REVERT: B 490 THR cc_start: 0.9281 (m) cc_final: 0.8904 (p) REVERT: B 493 MET cc_start: 0.9252 (tmm) cc_final: 0.8684 (tmm) REVERT: B 526 GLU cc_start: 0.8852 (mp0) cc_final: 0.8644 (mp0) REVERT: B 550 MET cc_start: 0.8107 (mtp) cc_final: 0.7800 (mtt) REVERT: B 570 MET cc_start: 0.8468 (tpp) cc_final: 0.6570 (tpp) REVERT: B 623 TRP cc_start: 0.8448 (t-100) cc_final: 0.8180 (t-100) REVERT: B 656 LEU cc_start: 0.9241 (mt) cc_final: 0.8990 (mt) REVERT: B 670 ILE cc_start: 0.9226 (mt) cc_final: 0.9013 (mt) REVERT: C 17 PHE cc_start: 0.9041 (p90) cc_final: 0.8365 (p90) REVERT: C 20 MET cc_start: 0.9410 (ppp) cc_final: 0.9190 (ppp) REVERT: C 21 PHE cc_start: 0.9119 (m-80) cc_final: 0.8553 (m-80) REVERT: C 46 TYR cc_start: 0.7856 (m-10) cc_final: 0.7647 (m-80) REVERT: C 74 MET cc_start: 0.9203 (mpp) cc_final: 0.8916 (mpp) REVERT: C 89 VAL cc_start: 0.7563 (t) cc_final: 0.7032 (t) REVERT: C 95 MET cc_start: 0.8346 (ttp) cc_final: 0.7619 (ttp) REVERT: C 174 TYR cc_start: 0.8904 (t80) cc_final: 0.7550 (t80) REVERT: C 178 PHE cc_start: 0.9049 (m-10) cc_final: 0.8517 (m-10) REVERT: C 226 GLU cc_start: 0.8836 (tt0) cc_final: 0.8632 (tt0) REVERT: C 231 LEU cc_start: 0.9068 (mt) cc_final: 0.8806 (mt) REVERT: C 274 ASP cc_start: 0.8892 (p0) cc_final: 0.8615 (p0) REVERT: D 29 PHE cc_start: 0.7166 (p90) cc_final: 0.6949 (p90) REVERT: D 96 MET cc_start: 0.7925 (tpt) cc_final: 0.7532 (tpt) REVERT: D 109 PHE cc_start: 0.8699 (m-10) cc_final: 0.8376 (m-80) REVERT: D 128 ASN cc_start: 0.8322 (t0) cc_final: 0.7966 (t0) REVERT: D 154 PHE cc_start: 0.7209 (m-80) cc_final: 0.6275 (m-80) REVERT: E 24 PHE cc_start: 0.8834 (m-80) cc_final: 0.8605 (m-80) REVERT: E 25 TRP cc_start: 0.8191 (p-90) cc_final: 0.7563 (p-90) REVERT: E 41 GLU cc_start: 0.8833 (pt0) cc_final: 0.8623 (tm-30) REVERT: E 46 MET cc_start: 0.8308 (tpp) cc_final: 0.8020 (tpp) REVERT: E 60 ASN cc_start: 0.9314 (t0) cc_final: 0.9021 (t0) REVERT: E 67 TYR cc_start: 0.8829 (m-10) cc_final: 0.8617 (m-80) REVERT: E 70 MET cc_start: 0.8132 (mmp) cc_final: 0.7544 (mpp) REVERT: E 93 LYS cc_start: 0.7518 (tptp) cc_final: 0.6695 (tptt) outliers start: 0 outliers final: 0 residues processed: 672 average time/residue: 0.1112 time to fit residues: 114.0569 Evaluate side-chains 560 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 115 optimal weight: 6.9990 chunk 152 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 107 optimal weight: 7.9990 chunk 142 optimal weight: 0.8980 chunk 188 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 78 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 474 GLN A 551 HIS ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN B 109 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** 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 = 0.3775 r_free = 0.3775 target = 0.132623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.095710 restraints weight = 43134.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.099086 restraints weight = 22440.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.101322 restraints weight = 14153.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.102734 restraints weight = 10034.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103876 restraints weight = 7880.528| |-----------------------------------------------------------------------------| r_work (final): 0.3303 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3303 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3303 r_free = 0.3303 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3303 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.6982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.098 17041 Z= 0.175 Angle : 0.657 11.818 23026 Z= 0.342 Chirality : 0.045 0.280 2464 Planarity : 0.004 0.058 2931 Dihedral : 10.044 144.886 2325 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.71 (0.19), residues: 2012 helix: 0.99 (0.15), residues: 1151 sheet: -0.28 (0.40), residues: 161 loop : -0.03 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.034 0.002 TYR A 683 PHE 0.043 0.002 PHE D 154 TRP 0.016 0.002 TRP A 623 HIS 0.006 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00389 (17038) covalent geometry : angle 0.65208 (23020) SS BOND : bond 0.00879 ( 3) SS BOND : angle 5.09544 ( 6) hydrogen bonds : bond 0.03876 ( 912) hydrogen bonds : angle 5.11054 ( 2664) *********************** 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 662 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 662 time to evaluate : 0.543 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: 0.8948 (tptp) cc_final: 0.8702 (tppt) REVERT: A 147 GLN cc_start: 0.8714 (tp-100) cc_final: 0.8001 (tp-100) REVERT: A 150 GLN cc_start: 0.8594 (tp-100) cc_final: 0.8363 (tp-100) REVERT: A 162 LYS cc_start: 0.9238 (tmtt) cc_final: 0.8970 (ttpt) REVERT: A 227 MET cc_start: 0.9239 (ptp) cc_final: 0.8984 (ptp) REVERT: A 228 LYS cc_start: 0.9083 (tptt) cc_final: 0.8651 (mptt) REVERT: A 230 LEU cc_start: 0.9744 (mt) cc_final: 0.9510 (mt) REVERT: A 250 TYR cc_start: 0.8185 (m-80) cc_final: 0.7743 (m-80) REVERT: A 254 PHE cc_start: 0.8740 (m-80) cc_final: 0.8278 (m-80) REVERT: A 290 GLU cc_start: 0.9107 (tm-30) cc_final: 0.8722 (tm-30) REVERT: A 291 LEU cc_start: 0.9488 (mm) cc_final: 0.9283 (mm) REVERT: A 301 PHE cc_start: 0.8982 (m-80) cc_final: 0.8512 (m-80) REVERT: A 346 LEU cc_start: 0.9467 (mt) cc_final: 0.9231 (mt) REVERT: A 358 ILE cc_start: 0.9249 (mm) cc_final: 0.8985 (mm) REVERT: A 367 VAL cc_start: 0.9620 (m) cc_final: 0.9406 (p) REVERT: A 390 GLN cc_start: 0.8889 (mt0) cc_final: 0.8619 (mt0) REVERT: A 421 GLU cc_start: 0.8619 (pp20) cc_final: 0.8248 (pp20) REVERT: A 498 TYR cc_start: 0.8738 (m-80) cc_final: 0.8523 (m-80) REVERT: A 501 GLN cc_start: 0.9017 (tt0) cc_final: 0.8572 (tt0) REVERT: A 515 ASP cc_start: 0.8918 (m-30) cc_final: 0.8513 (m-30) REVERT: A 570 MET cc_start: 0.8189 (ptm) cc_final: 0.7781 (ptt) REVERT: A 590 SER cc_start: 0.9471 (t) cc_final: 0.8777 (p) REVERT: A 615 MET cc_start: 0.8936 (mmm) cc_final: 0.8631 (mmm) REVERT: A 645 GLN cc_start: 0.8705 (tp40) cc_final: 0.8377 (tp40) REVERT: A 686 ARG cc_start: 0.8179 (ttm-80) cc_final: 0.7870 (mtp-110) REVERT: B 30 LYS cc_start: 0.9240 (tptt) cc_final: 0.8921 (tptp) REVERT: B 87 LYS cc_start: 0.9141 (tppt) cc_final: 0.8614 (ttmt) REVERT: B 112 LYS cc_start: 0.9398 (mmpt) cc_final: 0.9175 (mmmt) REVERT: B 127 LEU cc_start: 0.9778 (mt) cc_final: 0.9492 (mm) REVERT: B 129 PHE cc_start: 0.9131 (m-10) cc_final: 0.8855 (m-80) REVERT: B 138 LYS cc_start: 0.9434 (mtpt) cc_final: 0.9013 (mtmm) REVERT: B 145 ILE cc_start: 0.9383 (tp) cc_final: 0.9036 (tp) REVERT: B 147 GLN cc_start: 0.9214 (mt0) cc_final: 0.8397 (mt0) REVERT: B 150 GLN cc_start: 0.9516 (tp40) cc_final: 0.9293 (tp-100) REVERT: B 184 ARG cc_start: 0.9518 (tpp80) cc_final: 0.8741 (tpp80) REVERT: B 186 ILE cc_start: 0.9544 (mt) cc_final: 0.9298 (mt) REVERT: B 190 MET cc_start: 0.9332 (mtm) cc_final: 0.8888 (mtm) REVERT: B 228 LYS cc_start: 0.9553 (mmmt) cc_final: 0.9168 (mmmt) REVERT: B 231 ASP cc_start: 0.8414 (t70) cc_final: 0.6904 (t70) REVERT: B 232 ASN cc_start: 0.9124 (m110) cc_final: 0.8642 (m110) REVERT: B 235 ARG cc_start: 0.8788 (mtm-85) cc_final: 0.7787 (mtm-85) REVERT: B 256 ARG cc_start: 0.8291 (tmt170) cc_final: 0.8036 (ttp80) REVERT: B 258 ILE cc_start: 0.9419 (tp) cc_final: 0.9171 (tp) REVERT: B 286 ASP cc_start: 0.8498 (m-30) cc_final: 0.8050 (m-30) REVERT: B 348 MET cc_start: 0.9008 (ppp) cc_final: 0.8471 (ppp) REVERT: B 349 LEU cc_start: 0.9340 (mt) cc_final: 0.8631 (mt) REVERT: B 361 GLN cc_start: 0.8108 (tm-30) cc_final: 0.7472 (tm-30) REVERT: B 375 LYS cc_start: 0.8995 (mmmm) cc_final: 0.8470 (mmmm) REVERT: B 378 PHE cc_start: 0.9023 (p90) cc_final: 0.8642 (p90) REVERT: B 426 GLU cc_start: 0.8819 (tp30) cc_final: 0.7834 (tp30) REVERT: B 437 THR cc_start: 0.9455 (m) cc_final: 0.9092 (m) REVERT: B 466 MET cc_start: 0.8603 (ptt) cc_final: 0.8062 (ptt) REVERT: B 468 LEU cc_start: 0.9226 (tp) cc_final: 0.8942 (tp) REVERT: B 475 ASN cc_start: 0.9251 (m-40) cc_final: 0.8966 (m110) REVERT: B 490 THR cc_start: 0.9267 (m) cc_final: 0.8931 (p) REVERT: B 493 MET cc_start: 0.9273 (tmm) cc_final: 0.8492 (tmm) REVERT: B 498 TYR cc_start: 0.9003 (m-10) cc_final: 0.8767 (m-10) REVERT: B 515 ASP cc_start: 0.8889 (m-30) cc_final: 0.8381 (p0) REVERT: B 526 GLU cc_start: 0.8858 (mp0) cc_final: 0.8656 (mp0) REVERT: B 550 MET cc_start: 0.8009 (mtp) cc_final: 0.7674 (mtp) REVERT: B 570 MET cc_start: 0.8513 (tpp) cc_final: 0.6691 (tpp) REVERT: B 585 SER cc_start: 0.8752 (p) cc_final: 0.8529 (p) REVERT: B 612 TYR cc_start: 0.8416 (m-80) cc_final: 0.7926 (m-80) REVERT: B 656 LEU cc_start: 0.9229 (mt) cc_final: 0.8981 (mt) REVERT: C 17 PHE cc_start: 0.9066 (p90) cc_final: 0.8386 (p90) REVERT: C 20 MET cc_start: 0.9428 (ppp) cc_final: 0.9209 (ppp) REVERT: C 21 PHE cc_start: 0.9131 (m-80) cc_final: 0.8573 (m-80) REVERT: C 46 TYR cc_start: 0.7872 (m-10) cc_final: 0.7669 (m-80) REVERT: C 74 MET cc_start: 0.9264 (mpp) cc_final: 0.8908 (mpp) REVERT: C 89 VAL cc_start: 0.7538 (t) cc_final: 0.7019 (t) REVERT: C 95 MET cc_start: 0.8494 (ttp) cc_final: 0.7704 (ttp) REVERT: C 118 ILE cc_start: 0.9076 (mm) cc_final: 0.8634 (mm) REVERT: C 122 PHE cc_start: 0.8094 (m-80) cc_final: 0.7788 (m-80) REVERT: C 157 MET cc_start: 0.9350 (mtm) cc_final: 0.8765 (ptp) REVERT: C 174 TYR cc_start: 0.8849 (t80) cc_final: 0.7549 (t80) REVERT: C 178 PHE cc_start: 0.9045 (m-10) cc_final: 0.8484 (m-10) REVERT: C 226 GLU cc_start: 0.8824 (tt0) cc_final: 0.8615 (tt0) REVERT: C 231 LEU cc_start: 0.9129 (mt) cc_final: 0.8883 (mt) REVERT: C 274 ASP cc_start: 0.8871 (p0) cc_final: 0.8465 (p0) REVERT: D 25 ASN cc_start: 0.9321 (m-40) cc_final: 0.8798 (m-40) REVERT: D 29 PHE cc_start: 0.7176 (p90) cc_final: 0.6946 (p90) REVERT: D 92 PHE cc_start: 0.6948 (t80) cc_final: 0.6301 (t80) REVERT: D 96 MET cc_start: 0.7764 (tpt) cc_final: 0.7531 (tpt) REVERT: D 109 PHE cc_start: 0.8677 (m-10) cc_final: 0.8250 (m-80) REVERT: D 137 MET cc_start: 0.7980 (mmt) cc_final: 0.7385 (mtt) REVERT: D 238 ASN cc_start: 0.8436 (m110) cc_final: 0.7973 (m110) REVERT: D 273 PHE cc_start: 0.4213 (m-80) cc_final: 0.2824 (t80) REVERT: E 24 PHE cc_start: 0.8970 (m-80) cc_final: 0.8673 (m-80) REVERT: E 25 TRP cc_start: 0.8232 (p-90) cc_final: 0.7538 (p-90) REVERT: E 46 MET cc_start: 0.8339 (tpp) cc_final: 0.8064 (tpp) REVERT: E 60 ASN cc_start: 0.9289 (t0) cc_final: 0.8934 (t0) REVERT: E 67 TYR cc_start: 0.8845 (m-10) cc_final: 0.8632 (m-80) outliers start: 0 outliers final: 0 residues processed: 662 average time/residue: 0.1116 time to fit residues: 112.6960 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 : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 106 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 34 optimal weight: 0.8980 chunk 148 optimal weight: 20.0000 chunk 135 optimal weight: 0.9980 chunk 71 optimal weight: 7.9990 chunk 44 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 177 optimal weight: 2.9990 overall best weight: 1.3382 ------------------------------------------------------------------------------- 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 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 387 GLN ** 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 109 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.134174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.096668 restraints weight = 42721.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.100259 restraints weight = 21892.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.102564 restraints weight = 13528.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.104009 restraints weight = 9540.057| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3355 r_free = 0.3355 target = 0.105066 restraints weight = 7483.323| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3329 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3329 r_free = 0.3329 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3329 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.7171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.104 17041 Z= 0.155 Angle : 0.671 12.244 23026 Z= 0.347 Chirality : 0.045 0.244 2464 Planarity : 0.004 0.058 2931 Dihedral : 9.895 142.890 2325 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.64 (0.18), residues: 2012 helix: 0.94 (0.15), residues: 1156 sheet: -0.13 (0.40), residues: 161 loop : -0.13 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.026 0.002 TYR C 173 PHE 0.043 0.002 PHE A 234 TRP 0.015 0.001 TRP A 623 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00350 (17038) covalent geometry : angle 0.66531 (23020) SS BOND : bond 0.00759 ( 3) SS BOND : angle 5.60066 ( 6) hydrogen bonds : bond 0.03813 ( 912) hydrogen bonds : angle 5.06821 ( 2664) *********************** 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 : 0.447 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: A 117 ARG cc_start: 0.8344 (mmt180) cc_final: 0.8106 (mtt-85) REVERT: A 162 LYS cc_start: 0.9217 (tmtt) cc_final: 0.8990 (ttpt) REVERT: A 184 ARG cc_start: 0.9370 (mmm-85) cc_final: 0.9168 (mmm160) REVERT: A 209 LYS cc_start: 0.9407 (tttm) cc_final: 0.9167 (tttm) REVERT: A 227 MET cc_start: 0.9251 (ptp) cc_final: 0.9005 (ptp) REVERT: A 228 LYS cc_start: 0.9104 (tptt) cc_final: 0.8653 (tptt) REVERT: A 250 TYR cc_start: 0.8239 (m-80) cc_final: 0.7850 (m-80) REVERT: A 254 PHE cc_start: 0.8807 (m-80) cc_final: 0.8431 (m-80) REVERT: A 257 ASP cc_start: 0.8960 (m-30) cc_final: 0.8552 (m-30) REVERT: A 261 PHE cc_start: 0.9359 (t80) cc_final: 0.9100 (t80) REVERT: A 290 GLU cc_start: 0.9062 (tm-30) cc_final: 0.8519 (tm-30) REVERT: A 291 LEU cc_start: 0.9489 (mm) cc_final: 0.8947 (mm) REVERT: A 301 PHE cc_start: 0.8850 (m-80) cc_final: 0.8625 (m-80) REVERT: A 346 LEU cc_start: 0.9461 (mt) cc_final: 0.9219 (mt) REVERT: A 348 MET cc_start: 0.8829 (ptm) cc_final: 0.8614 (ptm) REVERT: A 358 ILE cc_start: 0.9267 (mm) cc_final: 0.9002 (mm) REVERT: A 390 GLN cc_start: 0.8862 (mt0) cc_final: 0.8606 (mt0) REVERT: A 421 GLU cc_start: 0.8598 (pp20) cc_final: 0.8229 (pp20) REVERT: A 498 TYR cc_start: 0.8764 (m-80) cc_final: 0.8527 (m-80) REVERT: A 515 ASP cc_start: 0.8874 (m-30) cc_final: 0.8469 (m-30) REVERT: A 558 TRP cc_start: 0.8810 (m100) cc_final: 0.8584 (m100) REVERT: A 570 MET cc_start: 0.8092 (ptm) cc_final: 0.7738 (ptt) REVERT: A 590 SER cc_start: 0.9417 (t) cc_final: 0.8987 (p) REVERT: A 615 MET cc_start: 0.8918 (mmm) cc_final: 0.8618 (mmm) REVERT: A 645 GLN cc_start: 0.8750 (tp40) cc_final: 0.8394 (tp40) REVERT: A 686 ARG cc_start: 0.8149 (ttm-80) cc_final: 0.7936 (mtp-110) REVERT: B 87 LYS cc_start: 0.9108 (tppt) cc_final: 0.8501 (ttmt) REVERT: B 120 ASP cc_start: 0.8851 (m-30) cc_final: 0.8624 (m-30) REVERT: B 127 LEU cc_start: 0.9770 (mt) cc_final: 0.9476 (mm) REVERT: B 129 PHE cc_start: 0.9122 (m-10) cc_final: 0.8830 (m-80) REVERT: B 138 LYS cc_start: 0.9430 (mtpt) cc_final: 0.9084 (mttt) REVERT: B 145 ILE cc_start: 0.9351 (tp) cc_final: 0.8971 (tp) REVERT: B 150 GLN cc_start: 0.9528 (tp40) cc_final: 0.9141 (tp-100) REVERT: B 184 ARG cc_start: 0.9507 (tpp80) cc_final: 0.8713 (tpp80) REVERT: B 186 ILE cc_start: 0.9545 (mt) cc_final: 0.9285 (mt) REVERT: B 190 MET cc_start: 0.9299 (mtm) cc_final: 0.8883 (mtm) REVERT: B 231 ASP cc_start: 0.8446 (t70) cc_final: 0.6997 (t70) REVERT: B 232 ASN cc_start: 0.9132 (m110) cc_final: 0.8692 (m110) REVERT: B 235 ARG cc_start: 0.8843 (mtm-85) cc_final: 0.8026 (mtm-85) REVERT: B 256 ARG cc_start: 0.8267 (tmt170) cc_final: 0.8023 (ttp80) REVERT: B 286 ASP cc_start: 0.8508 (m-30) cc_final: 0.8280 (m-30) REVERT: B 335 GLU cc_start: 0.7895 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 343 LEU cc_start: 0.9699 (mt) cc_final: 0.9491 (mm) REVERT: B 348 MET cc_start: 0.8995 (ppp) cc_final: 0.8449 (ppp) REVERT: B 349 LEU cc_start: 0.9328 (mt) cc_final: 0.8598 (mt) REVERT: B 361 GLN cc_start: 0.8052 (tm-30) cc_final: 0.7293 (tm-30) REVERT: B 375 LYS cc_start: 0.9016 (mmmm) cc_final: 0.8401 (mmmm) REVERT: B 378 PHE cc_start: 0.8964 (p90) cc_final: 0.8667 (p90) REVERT: B 426 GLU cc_start: 0.8877 (tp30) cc_final: 0.7729 (tp30) REVERT: B 437 THR cc_start: 0.9459 (m) cc_final: 0.9098 (m) REVERT: B 468 LEU cc_start: 0.9210 (tp) cc_final: 0.8971 (tp) REVERT: B 475 ASN cc_start: 0.9198 (m-40) cc_final: 0.8947 (m110) REVERT: B 493 MET cc_start: 0.9244 (tmm) cc_final: 0.8514 (tmm) REVERT: B 498 TYR cc_start: 0.9023 (m-10) cc_final: 0.8767 (m-10) REVERT: B 515 ASP cc_start: 0.8874 (m-30) cc_final: 0.8362 (p0) REVERT: B 550 MET cc_start: 0.8000 (mtp) cc_final: 0.7640 (mtp) REVERT: B 570 MET cc_start: 0.8507 (tpp) cc_final: 0.6572 (tpp) REVERT: B 588 GLN cc_start: 0.8474 (mm-40) cc_final: 0.8156 (mm-40) REVERT: B 612 TYR cc_start: 0.8480 (m-80) cc_final: 0.8005 (m-80) REVERT: B 623 TRP cc_start: 0.8759 (t-100) cc_final: 0.8346 (t-100) REVERT: B 656 LEU cc_start: 0.9216 (mt) cc_final: 0.8985 (mt) REVERT: B 670 ILE cc_start: 0.9292 (mt) cc_final: 0.9089 (mt) REVERT: C 17 PHE cc_start: 0.9045 (p90) cc_final: 0.8360 (p90) REVERT: C 20 MET cc_start: 0.9432 (ppp) cc_final: 0.9207 (ppp) REVERT: C 21 PHE cc_start: 0.9144 (m-80) cc_final: 0.8606 (m-80) REVERT: C 46 TYR cc_start: 0.7823 (m-10) cc_final: 0.7613 (m-80) REVERT: C 74 MET cc_start: 0.9253 (mpp) cc_final: 0.8906 (mpp) REVERT: C 89 VAL cc_start: 0.7578 (t) cc_final: 0.7079 (t) REVERT: C 95 MET cc_start: 0.8367 (ttp) cc_final: 0.7606 (ttp) REVERT: C 157 MET cc_start: 0.9353 (mtm) cc_final: 0.8749 (ptp) REVERT: C 174 TYR cc_start: 0.8844 (t80) cc_final: 0.7401 (t80) REVERT: C 178 PHE cc_start: 0.9061 (m-10) cc_final: 0.8475 (m-10) REVERT: C 226 GLU cc_start: 0.8839 (tt0) cc_final: 0.8620 (tt0) REVERT: C 231 LEU cc_start: 0.9136 (mt) cc_final: 0.8894 (mt) REVERT: C 274 ASP cc_start: 0.8950 (p0) cc_final: 0.8582 (p0) REVERT: D 25 ASN cc_start: 0.9331 (m-40) cc_final: 0.8923 (m-40) REVERT: D 29 PHE cc_start: 0.7362 (p90) cc_final: 0.7155 (p90) REVERT: D 115 THR cc_start: 0.8774 (p) cc_final: 0.8504 (t) REVERT: D 137 MET cc_start: 0.8072 (mmt) cc_final: 0.7584 (mtt) REVERT: D 238 ASN cc_start: 0.8469 (m110) cc_final: 0.8028 (m110) REVERT: E 24 PHE cc_start: 0.8947 (m-80) cc_final: 0.8694 (m-80) REVERT: E 25 TRP cc_start: 0.8118 (p-90) cc_final: 0.7411 (p-90) REVERT: E 42 LEU cc_start: 0.8171 (mt) cc_final: 0.7924 (mt) REVERT: E 46 MET cc_start: 0.8294 (tpp) cc_final: 0.8017 (tpp) REVERT: E 60 ASN cc_start: 0.9301 (t0) cc_final: 0.9027 (t0) outliers start: 0 outliers final: 0 residues processed: 650 average time/residue: 0.1135 time to fit residues: 111.9042 Evaluate side-chains 545 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 120 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 52 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 chunk 28 optimal weight: 0.9990 chunk 176 optimal weight: 0.8980 chunk 183 optimal weight: 3.9990 chunk 194 optimal weight: 10.0000 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 650 GLN ** A 675 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 312 GLN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** 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 = 0.3821 r_free = 0.3821 target = 0.135565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.098627 restraints weight = 43080.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.102144 restraints weight = 22573.155| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.104382 restraints weight = 14043.873| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.105920 restraints weight = 10011.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.106882 restraints weight = 7855.001| |-----------------------------------------------------------------------------| r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3339 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3339 r_free = 0.3339 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3340 r_free = 0.3340 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3340 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.7314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.102 17041 Z= 0.154 Angle : 0.671 12.040 23026 Z= 0.347 Chirality : 0.045 0.202 2464 Planarity : 0.004 0.058 2931 Dihedral : 9.848 143.417 2325 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.60 (0.18), residues: 2012 helix: 0.91 (0.15), residues: 1155 sheet: -0.22 (0.42), residues: 157 loop : -0.13 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 256 TYR 0.029 0.002 TYR D 105 PHE 0.037 0.002 PHE D 154 TRP 0.015 0.002 TRP B 623 HIS 0.009 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00348 (17038) covalent geometry : angle 0.66518 (23020) SS BOND : bond 0.00821 ( 3) SS BOND : angle 5.27577 ( 6) hydrogen bonds : bond 0.03811 ( 912) hydrogen bonds : angle 5.10251 ( 2664) ********************** 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 655 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 655 time to evaluate : 0.552 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: A 8 LYS cc_start: 0.9023 (tptp) cc_final: 0.8563 (tppt) REVERT: A 12 LEU cc_start: 0.9558 (mt) cc_final: 0.9261 (mt) REVERT: A 150 GLN cc_start: 0.8532 (tp-100) cc_final: 0.8110 (tp-100) REVERT: A 162 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8963 (ttpt) REVERT: A 184 ARG cc_start: 0.9380 (mmm-85) cc_final: 0.9149 (mmm160) REVERT: A 227 MET cc_start: 0.9255 (ptp) cc_final: 0.9041 (ptp) REVERT: A 228 LYS cc_start: 0.9069 (tptt) cc_final: 0.8608 (tptt) REVERT: A 250 TYR cc_start: 0.8197 (m-80) cc_final: 0.7820 (m-80) REVERT: A 261 PHE cc_start: 0.9383 (t80) cc_final: 0.9123 (t80) REVERT: A 290 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8426 (tm-30) REVERT: A 291 LEU cc_start: 0.9466 (mm) cc_final: 0.8889 (mm) REVERT: A 301 PHE cc_start: 0.8829 (m-80) cc_final: 0.8602 (m-80) REVERT: A 358 ILE cc_start: 0.9099 (mm) cc_final: 0.8872 (mm) REVERT: A 367 VAL cc_start: 0.9574 (m) cc_final: 0.9357 (p) REVERT: A 390 GLN cc_start: 0.8864 (mt0) cc_final: 0.8578 (mt0) REVERT: A 421 GLU cc_start: 0.8679 (pp20) cc_final: 0.8307 (pp20) REVERT: A 456 LYS cc_start: 0.9072 (ptpp) cc_final: 0.8753 (ptpp) REVERT: A 498 TYR cc_start: 0.8818 (m-80) cc_final: 0.8555 (m-80) REVERT: A 501 GLN cc_start: 0.8955 (tt0) cc_final: 0.8566 (tm-30) REVERT: A 515 ASP cc_start: 0.8858 (m-30) cc_final: 0.8447 (m-30) REVERT: A 570 MET cc_start: 0.8127 (ptm) cc_final: 0.7776 (ptt) REVERT: A 590 SER cc_start: 0.9473 (t) cc_final: 0.8824 (p) REVERT: A 615 MET cc_start: 0.8903 (mmm) cc_final: 0.8594 (mmm) REVERT: A 634 MET cc_start: 0.8558 (mmt) cc_final: 0.8078 (tpp) REVERT: A 645 GLN cc_start: 0.8734 (tp40) cc_final: 0.8380 (tp40) REVERT: A 661 THR cc_start: 0.9599 (p) cc_final: 0.9139 (p) REVERT: A 686 ARG cc_start: 0.8114 (ttm-80) cc_final: 0.7895 (mtp-110) REVERT: B 87 LYS cc_start: 0.9104 (tppt) cc_final: 0.8547 (tptp) REVERT: B 112 LYS cc_start: 0.9389 (mmpt) cc_final: 0.9189 (mmmt) REVERT: B 120 ASP cc_start: 0.8821 (m-30) cc_final: 0.8617 (m-30) REVERT: B 127 LEU cc_start: 0.9772 (mt) cc_final: 0.9487 (mm) REVERT: B 129 PHE cc_start: 0.9127 (m-10) cc_final: 0.8864 (m-80) REVERT: B 138 LYS cc_start: 0.9423 (mtpt) cc_final: 0.9080 (mttt) REVERT: B 147 GLN cc_start: 0.9080 (mt0) cc_final: 0.8093 (mm-40) REVERT: B 184 ARG cc_start: 0.9520 (tpp80) cc_final: 0.8666 (tpp80) REVERT: B 186 ILE cc_start: 0.9538 (mt) cc_final: 0.9291 (mt) REVERT: B 190 MET cc_start: 0.9357 (mtm) cc_final: 0.8943 (mtm) REVERT: B 227 MET cc_start: 0.9056 (mtm) cc_final: 0.8820 (mtm) REVERT: B 231 ASP cc_start: 0.8466 (t70) cc_final: 0.7135 (t70) REVERT: B 232 ASN cc_start: 0.9127 (m110) cc_final: 0.8633 (m110) REVERT: B 235 ARG cc_start: 0.8830 (mtm-85) cc_final: 0.7861 (mtm-85) REVERT: B 256 ARG cc_start: 0.8285 (tmt170) cc_final: 0.8020 (ttp80) REVERT: B 335 GLU cc_start: 0.7936 (tm-30) cc_final: 0.7651 (tm-30) REVERT: B 343 LEU cc_start: 0.9736 (mt) cc_final: 0.9526 (mm) REVERT: B 348 MET cc_start: 0.9014 (ppp) cc_final: 0.8465 (ppp) REVERT: B 349 LEU cc_start: 0.9325 (mt) cc_final: 0.8603 (mt) REVERT: B 361 GLN cc_start: 0.8039 (tm-30) cc_final: 0.7244 (tm-30) REVERT: B 375 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8390 (mmmm) REVERT: B 378 PHE cc_start: 0.8965 (p90) cc_final: 0.8688 (p90) REVERT: B 384 GLU cc_start: 0.7991 (pp20) cc_final: 0.7401 (pp20) REVERT: B 426 GLU cc_start: 0.8863 (tp30) cc_final: 0.7914 (tp30) REVERT: B 427 LYS cc_start: 0.9093 (ptpp) cc_final: 0.8834 (ptpp) REVERT: B 437 THR cc_start: 0.9451 (m) cc_final: 0.9129 (m) REVERT: B 446 ARG cc_start: 0.7296 (mmm160) cc_final: 0.7043 (mmp80) REVERT: B 468 LEU cc_start: 0.9230 (tp) cc_final: 0.8965 (tp) REVERT: B 475 ASN cc_start: 0.9207 (m-40) cc_final: 0.8940 (m110) REVERT: B 493 MET cc_start: 0.9236 (tmm) cc_final: 0.8530 (tmm) REVERT: B 515 ASP cc_start: 0.8890 (m-30) cc_final: 0.8368 (p0) REVERT: B 550 MET cc_start: 0.8040 (mtp) cc_final: 0.7687 (mtp) REVERT: B 570 MET cc_start: 0.8493 (tpp) cc_final: 0.6588 (tpp) REVERT: B 571 TYR cc_start: 0.8848 (t80) cc_final: 0.8643 (t80) REVERT: B 599 GLU cc_start: 0.8784 (mp0) cc_final: 0.8583 (pm20) REVERT: B 612 TYR cc_start: 0.8523 (m-80) cc_final: 0.7696 (m-80) REVERT: B 623 TRP cc_start: 0.8877 (t-100) cc_final: 0.8454 (t-100) REVERT: B 656 LEU cc_start: 0.9177 (mt) cc_final: 0.8932 (mt) REVERT: C 17 PHE cc_start: 0.9109 (p90) cc_final: 0.8409 (p90) REVERT: C 20 MET cc_start: 0.9439 (ppp) cc_final: 0.9211 (ppp) REVERT: C 21 PHE cc_start: 0.9139 (m-80) cc_final: 0.8562 (m-80) REVERT: C 68 GLU cc_start: 0.8972 (mp0) cc_final: 0.8537 (pm20) REVERT: C 74 MET cc_start: 0.9212 (mpp) cc_final: 0.8872 (mpp) REVERT: C 89 VAL cc_start: 0.7442 (t) cc_final: 0.6954 (t) REVERT: C 95 MET cc_start: 0.8950 (tmm) cc_final: 0.8424 (tmm) REVERT: C 100 VAL cc_start: 0.8567 (t) cc_final: 0.7978 (t) REVERT: C 157 MET cc_start: 0.9417 (mtm) cc_final: 0.8738 (ptp) REVERT: C 174 TYR cc_start: 0.8860 (t80) cc_final: 0.7516 (t80) REVERT: C 178 PHE cc_start: 0.9037 (m-10) cc_final: 0.8444 (m-10) REVERT: C 197 ASP cc_start: 0.9610 (m-30) cc_final: 0.9306 (m-30) REVERT: C 226 GLU cc_start: 0.8891 (tt0) cc_final: 0.8674 (tt0) REVERT: C 231 LEU cc_start: 0.9147 (mt) cc_final: 0.8903 (mt) REVERT: C 274 ASP cc_start: 0.9006 (p0) cc_final: 0.8665 (p0) REVERT: D 25 ASN cc_start: 0.9281 (m-40) cc_final: 0.8846 (m-40) REVERT: D 29 PHE cc_start: 0.7465 (p90) cc_final: 0.7173 (p90) REVERT: D 92 PHE cc_start: 0.6861 (t80) cc_final: 0.6292 (t80) REVERT: D 115 THR cc_start: 0.8762 (p) cc_final: 0.8438 (t) REVERT: D 128 ASN cc_start: 0.8520 (t0) cc_final: 0.8169 (t0) REVERT: D 137 MET cc_start: 0.8164 (mmt) cc_final: 0.7718 (mtt) REVERT: D 218 GLU cc_start: 0.9028 (mm-30) cc_final: 0.8686 (tm-30) REVERT: E 24 PHE cc_start: 0.9014 (m-80) cc_final: 0.8644 (m-80) REVERT: E 25 TRP cc_start: 0.8220 (p-90) cc_final: 0.7482 (p-90) REVERT: E 46 MET cc_start: 0.8116 (tpp) cc_final: 0.7792 (tpp) REVERT: E 60 ASN cc_start: 0.9347 (t0) cc_final: 0.9125 (t0) outliers start: 0 outliers final: 0 residues processed: 655 average time/residue: 0.1154 time to fit residues: 115.8144 Evaluate side-chains 551 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 72 optimal weight: 2.9990 chunk 62 optimal weight: 6.9990 chunk 96 optimal weight: 2.9990 chunk 121 optimal weight: 0.6980 chunk 127 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 89 optimal weight: 4.9990 chunk 51 optimal weight: 9.9990 chunk 141 optimal weight: 5.9990 chunk 58 optimal weight: 4.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 ASN ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN C 132 GLN C 270 ASN ** D 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 249 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133336 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.097021 restraints weight = 43458.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100326 restraints weight = 23464.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102379 restraints weight = 14864.169| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.103902 restraints weight = 10728.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.104819 restraints weight = 8443.166| |-----------------------------------------------------------------------------| r_work (final): 0.3316 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3305 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3305 r_free = 0.3305 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3305 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.102 17041 Z= 0.190 Angle : 0.695 11.890 23026 Z= 0.361 Chirality : 0.045 0.181 2464 Planarity : 0.004 0.056 2931 Dihedral : 9.887 145.633 2325 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.53 (0.18), residues: 2012 helix: 0.85 (0.15), residues: 1154 sheet: -0.19 (0.48), residues: 127 loop : -0.18 (0.23), residues: 731 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 225 TYR 0.029 0.002 TYR D 105 PHE 0.036 0.002 PHE D 154 TRP 0.030 0.003 TRP A 558 HIS 0.008 0.001 HIS C 201 Details of bonding type rmsd covalent geometry : bond 0.00423 (17038) covalent geometry : angle 0.68908 (23020) SS BOND : bond 0.00790 ( 3) SS BOND : angle 5.44869 ( 6) hydrogen bonds : bond 0.03918 ( 912) hydrogen bonds : angle 5.17422 ( 2664) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3333.52 seconds wall clock time: 58 minutes 30.21 seconds (3510.21 seconds total)