Starting phenix.real_space_refine on Sun May 18 04:24:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.cif Found real_map, /net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.map" model { file = "/net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9by0_45016/05_2025/9by0_45016.cif" } resolution = 4.19 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Mn 4 7.51 5 P 16 5.49 5 Mg 2 5.21 5 S 87 5.16 5 C 10641 2.51 5 N 2712 2.21 5 O 3216 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 69 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 16678 Number of models: 1 Model: "" Number of chains: 9 Chain: "A" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "B" Number of atoms: 5554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 683, 5554 Classifications: {'peptide': 683} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 665} Chain: "C" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "D" Number of atoms: 2360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2360 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 7, 'TRANS': 279} Chain breaks: 1 Chain: "E" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 668 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 80} Chain: "A" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 89 Unusual residues: {' MG': 1, 'ATP': 1, 'GDP': 1, 'TTP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N SER D 187 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 187 " occ=0.50 residue: pdb=" N SER D 253 " occ=0.50 ... (4 atoms not shown) pdb=" OG SER D 253 " occ=0.50 residue: pdb="MN MN C 401 " occ=0.85 residue: pdb="MN MN C 402 " occ=0.85 Time building chain proxies: 9.96, per 1000 atoms: 0.60 Number of scatterers: 16678 At special positions: 0 Unit cell: (94.302, 137.904, 143.988, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Mn 4 24.99 S 87 16.00 P 16 15.00 Mg 2 11.99 O 3216 8.00 N 2712 7.00 C 10641 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 170 " - pdb=" SG CYS A 409 " distance=2.03 Simple disulfide: pdb=" SG CYS B 170 " - pdb=" SG CYS B 409 " distance=2.03 Simple disulfide: pdb=" SG CYS E 29 " - pdb=" SG CYS E 32 " distance=2.66 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.50 Conformation dependent library (CDL) restraints added in 2.1 seconds 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3848 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 11 sheets defined 63.4% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.89 Creating SS restraints... Processing helix chain 'A' and resid 7 through 14 Processing helix chain 'A' and resid 15 through 17 No H-bonds generated for 'chain 'A' and resid 15 through 17' Processing helix chain 'A' and resid 27 through 40 removed outlier: 3.771A pdb=" N GLU A 31 " --> pdb=" O ASP A 27 " (cutoff:3.500A) Processing helix chain 'A' and resid 50 through 61 Processing helix chain 'A' and resid 65 through 71 removed outlier: 4.260A pdb=" N LEU A 69 " --> pdb=" O GLU A 65 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LEU A 71 " --> pdb=" O GLU A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 87 removed outlier: 3.787A pdb=" N LYS A 87 " --> pdb=" O THR A 83 " (cutoff:3.500A) Processing helix chain 'A' and resid 93 through 104 removed outlier: 3.639A pdb=" N ALA A 97 " --> pdb=" O SER A 93 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 removed outlier: 3.525A pdb=" N ASN A 131 " --> pdb=" O LEU A 127 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 146 Processing helix chain 'A' and resid 152 through 159 Processing helix chain 'A' and resid 178 through 194 Processing helix chain 'A' and resid 222 through 237 removed outlier: 4.065A pdb=" N VAL A 226 " --> pdb=" O GLY A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 242 Processing helix chain 'A' and resid 257 through 264 removed outlier: 3.527A pdb=" N THR A 264 " --> pdb=" O ASP A 260 " (cutoff:3.500A) Processing helix chain 'A' and resid 285 through 294 removed outlier: 3.662A pdb=" N VAL A 289 " --> pdb=" O PRO A 285 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 311 Processing helix chain 'A' and resid 313 through 317 Processing helix chain 'A' and resid 318 through 328 removed outlier: 5.965A pdb=" N ASP A 324 " --> pdb=" O ASN A 320 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N LYS A 325 " --> pdb=" O GLU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 354 Processing helix chain 'A' and resid 361 through 367 removed outlier: 4.231A pdb=" N VAL A 367 " --> pdb=" O ASN A 363 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 424 through 443 Processing helix chain 'A' and resid 448 through 459 Processing helix chain 'A' and resid 467 through 475 Processing helix chain 'A' and resid 481 through 511 Processing helix chain 'A' and resid 520 through 525 Processing helix chain 'A' and resid 528 through 534 Processing helix chain 'A' and resid 540 through 547 removed outlier: 3.567A pdb=" N PHE A 547 " --> pdb=" O ILE A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 554 through 569 Processing helix chain 'A' and resid 582 through 588 removed outlier: 4.060A pdb=" N TYR A 586 " --> pdb=" O GLY A 582 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N VAL A 587 " --> pdb=" O SER A 583 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 632 Processing helix chain 'A' and resid 633 through 646 Processing helix chain 'A' and resid 663 through 677 Processing helix chain 'B' and resid 7 through 15 Processing helix chain 'B' and resid 27 through 40 removed outlier: 3.613A pdb=" N GLU B 31 " --> pdb=" O ASP B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 50 through 61 Processing helix chain 'B' and resid 65 through 71 removed outlier: 4.044A pdb=" N LEU B 69 " --> pdb=" O GLU B 65 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU B 71 " --> pdb=" O GLU B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 86 Processing helix chain 'B' and resid 93 through 104 removed outlier: 3.633A pdb=" N ALA B 97 " --> pdb=" O SER B 93 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 131 Processing helix chain 'B' and resid 133 through 146 Processing helix chain 'B' and resid 152 through 159 Processing helix chain 'B' and resid 178 through 195 Processing helix chain 'B' and resid 221 through 237 removed outlier: 3.879A pdb=" N GLY B 225 " --> pdb=" O LYS B 221 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 242 Processing helix chain 'B' and resid 257 through 264 removed outlier: 3.514A pdb=" N THR B 264 " --> pdb=" O ASP B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 295 removed outlier: 3.647A pdb=" N VAL B 289 " --> pdb=" O PRO B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 311 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'B' and resid 318 through 328 removed outlier: 5.482A pdb=" N ASP B 324 " --> pdb=" O ASN B 320 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N LYS B 325 " --> pdb=" O GLU B 321 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 354 Processing helix chain 'B' and resid 361 through 366 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 424 through 443 Processing helix chain 'B' and resid 448 through 459 Processing helix chain 'B' and resid 467 through 475 Processing helix chain 'B' and resid 481 through 511 Processing helix chain 'B' and resid 520 through 525 Processing helix chain 'B' and resid 528 through 534 Processing helix chain 'B' and resid 540 through 547 removed outlier: 3.562A pdb=" N LEU B 546 " --> pdb=" O LYS B 542 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE B 547 " --> pdb=" O ILE B 543 " (cutoff:3.500A) Processing helix chain 'B' and resid 554 through 569 Processing helix chain 'B' and resid 583 through 588 removed outlier: 4.256A pdb=" N VAL B 587 " --> pdb=" O SER B 583 " (cutoff:3.500A) Processing helix chain 'B' and resid 628 through 632 Processing helix chain 'B' and resid 633 through 646 Processing helix chain 'B' and resid 663 through 678 Processing helix chain 'C' and resid 17 through 28 Processing helix chain 'C' and resid 31 through 35 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'C' and resid 48 through 72 Processing helix chain 'C' and resid 72 through 81 Processing helix chain 'C' and resid 83 through 100 Processing helix chain 'C' and resid 100 through 113 removed outlier: 3.545A pdb=" N TYR C 105 " --> pdb=" O HIS C 101 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER C 106 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 114 through 128 removed outlier: 3.514A pdb=" N LYS C 126 " --> pdb=" O PHE C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 144 Processing helix chain 'C' and resid 149 through 166 Processing helix chain 'C' and resid 168 through 180 removed outlier: 4.935A pdb=" N TYR C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) Proline residue: C 175 - end of helix Processing helix chain 'C' and resid 184 through 214 removed outlier: 3.566A pdb=" N ILE C 200 " --> pdb=" O ARG C 196 " (cutoff:3.500A) Processing helix chain 'C' and resid 217 through 248 Processing helix chain 'C' and resid 249 through 251 No H-bonds generated for 'chain 'C' and resid 249 through 251' Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 283 through 289 Processing helix chain 'C' and resid 316 through 320 removed outlier: 3.812A pdb=" N PHE C 320 " --> pdb=" O ASP C 317 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 28 Processing helix chain 'D' and resid 31 through 35 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 45 Processing helix chain 'D' and resid 48 through 72 Processing helix chain 'D' and resid 72 through 81 Processing helix chain 'D' and resid 83 through 100 Processing helix chain 'D' and resid 100 through 113 Processing helix chain 'D' and resid 114 through 128 Processing helix chain 'D' and resid 128 through 144 Processing helix chain 'D' and resid 149 through 166 Processing helix chain 'D' and resid 168 through 180 removed outlier: 4.875A pdb=" N TYR D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) Proline residue: D 175 - end of helix Processing helix chain 'D' and resid 184 through 214 Processing helix chain 'D' and resid 217 through 248 Processing helix chain 'D' and resid 249 through 251 No H-bonds generated for 'chain 'D' and resid 249 through 251' Processing helix chain 'D' and resid 252 through 271 Processing helix chain 'D' and resid 283 through 290 Processing helix chain 'E' and resid 29 through 47 Proline residue: E 37 - end of helix Processing helix chain 'E' and resid 60 through 67 Processing helix chain 'E' and resid 92 through 102 removed outlier: 3.528A pdb=" N LYS E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 149 through 151 removed outlier: 6.234A pdb=" N GLY A 412 " --> pdb=" O GLY A 464 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N MET A 466 " --> pdb=" O GLY A 412 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N LEU A 414 " --> pdb=" O MET A 466 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 407 through 408 removed outlier: 6.021A pdb=" N PHE A 171 " --> pdb=" O SER A 200 " (cutoff:3.500A) removed outlier: 7.540A pdb=" N ASN A 202 " --> pdb=" O PHE A 171 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N LEU A 173 " --> pdb=" O ASN A 202 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N VAL A 199 " --> pdb=" O ALA A 248 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N TYR A 250 " --> pdb=" O VAL A 199 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N LEU A 201 " --> pdb=" O TYR A 250 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASN A 252 " --> pdb=" O LEU A 201 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N GLY A 247 " --> pdb=" O SER A 279 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N GLY A 281 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N ALA A 249 " --> pdb=" O GLY A 281 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N VAL A 283 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU A 251 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 298 through 301 Processing sheet with id=AA4, first strand: chain 'A' and resid 601 through 606 Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 659 Processing sheet with id=AA6, first strand: chain 'B' and resid 149 through 151 removed outlier: 6.817A pdb=" N GLY B 462 " --> pdb=" O SER B 408 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ASN B 410 " --> pdb=" O GLY B 462 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N GLY B 464 " --> pdb=" O ASN B 410 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLY B 412 " --> pdb=" O GLY B 464 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N MET B 466 " --> pdb=" O GLY B 412 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N LEU B 414 " --> pdb=" O MET B 466 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 149 through 151 removed outlier: 3.879A pdb=" N CYS B 170 " --> pdb=" O CYS B 409 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 199 " --> pdb=" O ALA B 248 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N TYR B 250 " --> pdb=" O VAL B 199 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N LEU B 201 " --> pdb=" O TYR B 250 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N ASN B 252 " --> pdb=" O LEU B 201 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 298 through 301 Processing sheet with id=AA9, first strand: chain 'B' and resid 601 through 605 Processing sheet with id=AB1, first strand: chain 'B' and resid 655 through 659 Processing sheet with id=AB2, first strand: chain 'E' and resid 51 through 56 removed outlier: 6.467A pdb=" N LYS E 79 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N VAL E 83 " --> pdb=" O LYS E 79 " (cutoff:3.500A) 914 hydrogen bonds defined for protein. 2664 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.19 Time building geometry restraints manager: 5.21 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: 1.020 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: 0.660 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 38.560 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6353 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.629 17041 Z= 0.416 Angle : 0.841 18.197 23026 Z= 0.527 Chirality : 0.061 0.722 2464 Planarity : 0.004 0.060 2931 Dihedral : 17.534 148.635 6399 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 1.40 % Allowed : 16.27 % Favored : 82.34 % Cbeta Deviations : 0.21 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.18), residues: 2012 helix: 0.63 (0.14), residues: 1157 sheet: -0.31 (0.37), residues: 179 loop : 0.42 (0.24), residues: 676 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.077 0.005 TRP E 25 HIS 0.006 0.001 HIS C 254 PHE 0.120 0.003 PHE B 624 TYR 0.029 0.002 TYR E 67 ARG 0.007 0.000 ARG A 331 Details of bonding type rmsd hydrogen bonds : bond 0.16741 ( 912) hydrogen bonds : angle 6.70349 ( 2664) SS BOND : bond 0.36331 ( 3) SS BOND : angle 6.07971 ( 6) covalent geometry : bond 0.00602 (17038) covalent geometry : angle 0.83524 (23020) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 968 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 943 time to evaluate : 1.859 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 VAL cc_start: 0.8664 (t) cc_final: 0.8426 (p) REVERT: A 68 PHE cc_start: 0.7989 (p90) cc_final: 0.7642 (p90) REVERT: A 171 PHE cc_start: 0.8288 (m-80) cc_final: 0.7976 (m-80) REVERT: A 202 ASN cc_start: 0.8911 (t0) cc_final: 0.8660 (t0) REVERT: A 367 VAL cc_start: 0.8707 (m) cc_final: 0.8307 (p) REVERT: A 378 PHE cc_start: 0.8293 (p90) cc_final: 0.7930 (p90) REVERT: A 483 GLU cc_start: 0.8151 (mp0) cc_final: 0.7913 (mp0) REVERT: A 655 THR cc_start: 0.9457 (m) cc_final: 0.9200 (t) REVERT: B 17 MET cc_start: 0.7011 (mmm) cc_final: 0.6213 (mmm) REVERT: B 41 ILE cc_start: 0.8797 (mm) cc_final: 0.8316 (mt) REVERT: B 46 VAL cc_start: 0.8358 (OUTLIER) cc_final: 0.8143 (m) REVERT: B 51 LEU cc_start: 0.7905 (tp) cc_final: 0.7640 (tp) REVERT: B 127 LEU cc_start: 0.9293 (mt) cc_final: 0.9060 (mt) REVERT: B 129 PHE cc_start: 0.7800 (m-10) cc_final: 0.7473 (m-80) REVERT: B 177 ASP cc_start: 0.8336 (t0) cc_final: 0.7989 (t0) REVERT: B 204 SER cc_start: 0.8620 (m) cc_final: 0.8397 (t) REVERT: B 230 LEU cc_start: 0.9308 (mt) cc_final: 0.9080 (mt) REVERT: B 315 ASP cc_start: 0.8578 (p0) cc_final: 0.8314 (t0) REVERT: B 322 MET cc_start: 0.7356 (mmm) cc_final: 0.6949 (mmm) REVERT: B 349 LEU cc_start: 0.8462 (mt) cc_final: 0.8151 (mp) REVERT: B 364 VAL cc_start: 0.8818 (t) cc_final: 0.8597 (t) REVERT: B 384 GLU cc_start: 0.8215 (pp20) cc_final: 0.7610 (pm20) REVERT: B 385 VAL cc_start: 0.8660 (t) cc_final: 0.8392 (t) REVERT: B 417 LEU cc_start: 0.8368 (tp) cc_final: 0.8053 (tp) REVERT: B 500 ILE cc_start: 0.9353 (mt) cc_final: 0.8767 (mt) REVERT: B 531 TYR cc_start: 0.6004 (m-80) cc_final: 0.5682 (m-80) REVERT: B 550 MET cc_start: 0.7101 (mtm) cc_final: 0.6594 (mtp) REVERT: B 574 TYR cc_start: 0.8035 (m-80) cc_final: 0.7820 (m-80) REVERT: B 576 LEU cc_start: 0.8710 (mt) cc_final: 0.8327 (mt) REVERT: B 644 ILE cc_start: 0.8828 (mt) cc_final: 0.8593 (mt) REVERT: B 687 THR cc_start: 0.7230 (p) cc_final: 0.6959 (p) REVERT: C 89 VAL cc_start: 0.6220 (t) cc_final: 0.5263 (t) REVERT: C 101 HIS cc_start: 0.5472 (m170) cc_final: 0.4827 (m-70) REVERT: C 131 LEU cc_start: 0.6464 (OUTLIER) cc_final: 0.6050 (tp) REVERT: C 153 LEU cc_start: 0.7009 (tp) cc_final: 0.6724 (tp) REVERT: C 163 LEU cc_start: 0.6154 (tt) cc_final: 0.5807 (tp) REVERT: C 268 LEU cc_start: 0.4343 (mt) cc_final: 0.4057 (mt) REVERT: D 185 MET cc_start: 0.6866 (mmm) cc_final: 0.6551 (tpp) REVERT: D 265 ASN cc_start: 0.4744 (m-40) cc_final: 0.4472 (m110) REVERT: E 25 TRP cc_start: 0.8230 (p-90) cc_final: 0.7924 (p-90) REVERT: E 78 LEU cc_start: 0.6579 (mp) cc_final: 0.5542 (tt) outliers start: 25 outliers final: 3 residues processed: 948 average time/residue: 0.3235 time to fit residues: 448.6941 Evaluate side-chains 637 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 632 time to evaluate : 2.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 168 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 10.0000 chunk 102 optimal weight: 1.9990 chunk 80 optimal weight: 5.9990 chunk 156 optimal weight: 0.8980 chunk 60 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 181 optimal weight: 6.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 568 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 34 HIS B 61 ASN B 191 GLN B 304 HIS ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 320 ASN ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN C 216 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.130068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.092077 restraints weight = 41580.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.095707 restraints weight = 21491.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.098148 restraints weight = 13485.630| |-----------------------------------------------------------------------------| r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3238 r_free = 0.3238 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3238 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7391 moved from start: 0.4502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 17041 Z= 0.244 Angle : 0.711 16.543 23026 Z= 0.374 Chirality : 0.045 0.186 2464 Planarity : 0.005 0.046 2931 Dihedral : 10.704 150.679 2325 Min Nonbonded Distance : 1.728 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.34 % Allowed : 2.96 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.18), residues: 2012 helix: 1.25 (0.15), residues: 1158 sheet: -0.15 (0.39), residues: 155 loop : 0.49 (0.24), residues: 699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 623 HIS 0.009 0.001 HIS B 438 PHE 0.033 0.002 PHE C 168 TYR 0.026 0.002 TYR D 105 ARG 0.006 0.001 ARG B 235 Details of bonding type rmsd hydrogen bonds : bond 0.04805 ( 912) hydrogen bonds : angle 5.16462 ( 2664) SS BOND : bond 0.00458 ( 3) SS BOND : angle 8.28576 ( 6) covalent geometry : bond 0.00519 (17038) covalent geometry : angle 0.69889 (23020) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 732 time to evaluate : 1.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 GLU cc_start: 0.8530 (mp0) cc_final: 0.8236 (mm-30) REVERT: A 147 GLN cc_start: 0.8618 (tp-100) cc_final: 0.7947 (tp40) REVERT: A 195 LEU cc_start: 0.9398 (mt) cc_final: 0.9157 (mt) REVERT: A 223 VAL cc_start: 0.9498 (m) cc_final: 0.9201 (p) REVERT: A 224 VAL cc_start: 0.9489 (m) cc_final: 0.9242 (m) REVERT: A 301 PHE cc_start: 0.9001 (m-80) cc_final: 0.8773 (m-80) REVERT: A 338 ASN cc_start: 0.9555 (t0) cc_final: 0.7875 (t0) REVERT: A 341 LYS cc_start: 0.9692 (mmtp) cc_final: 0.9379 (mmtp) REVERT: A 346 LEU cc_start: 0.9534 (mt) cc_final: 0.9327 (mt) REVERT: A 360 PHE cc_start: 0.8503 (m-80) cc_final: 0.7952 (m-80) REVERT: A 367 VAL cc_start: 0.9515 (m) cc_final: 0.9226 (p) REVERT: A 421 GLU cc_start: 0.8228 (pp20) cc_final: 0.7903 (pp20) REVERT: A 453 ARG cc_start: 0.9234 (ttt-90) cc_final: 0.8829 (ttt-90) REVERT: A 466 MET cc_start: 0.8397 (ptt) cc_final: 0.8006 (ptt) REVERT: A 475 ASN cc_start: 0.8368 (m110) cc_final: 0.8030 (m110) REVERT: A 509 GLU cc_start: 0.8877 (tm-30) cc_final: 0.8435 (tm-30) REVERT: A 518 GLU cc_start: 0.8932 (pp20) cc_final: 0.8650 (pp20) REVERT: A 528 PHE cc_start: 0.8470 (m-10) cc_final: 0.8147 (m-80) REVERT: A 558 TRP cc_start: 0.8996 (m100) cc_final: 0.8351 (m100) REVERT: A 639 ASP cc_start: 0.8904 (m-30) cc_final: 0.8593 (m-30) REVERT: A 655 THR cc_start: 0.8990 (m) cc_final: 0.8609 (t) REVERT: A 658 LEU cc_start: 0.9574 (mp) cc_final: 0.9323 (mp) REVERT: B 18 ILE cc_start: 0.9374 (mm) cc_final: 0.8805 (mm) REVERT: B 41 ILE cc_start: 0.9468 (mm) cc_final: 0.9264 (mt) REVERT: B 127 LEU cc_start: 0.9790 (mt) cc_final: 0.9536 (mm) REVERT: B 135 GLU cc_start: 0.9169 (mp0) cc_final: 0.8841 (pm20) REVERT: B 147 GLN cc_start: 0.9045 (mt0) cc_final: 0.8618 (mt0) REVERT: B 150 GLN cc_start: 0.9382 (tp-100) cc_final: 0.8858 (tp-100) REVERT: B 156 PHE cc_start: 0.9272 (t80) cc_final: 0.9034 (t80) REVERT: B 186 ILE cc_start: 0.9669 (mt) cc_final: 0.9334 (mt) REVERT: B 190 MET cc_start: 0.9343 (mtm) cc_final: 0.8888 (mtm) REVERT: B 227 MET cc_start: 0.9200 (mtp) cc_final: 0.8965 (mtp) REVERT: B 256 ARG cc_start: 0.8424 (tmt170) cc_final: 0.8088 (ttp80) REVERT: B 257 ASP cc_start: 0.8483 (m-30) cc_final: 0.7682 (m-30) REVERT: B 260 ASP cc_start: 0.9273 (m-30) cc_final: 0.9054 (p0) REVERT: B 286 ASP cc_start: 0.8431 (m-30) cc_final: 0.8230 (m-30) REVERT: B 317 MET cc_start: 0.8857 (mtp) cc_final: 0.8557 (mtt) REVERT: B 348 MET cc_start: 0.9058 (ppp) cc_final: 0.8470 (ppp) REVERT: B 349 LEU cc_start: 0.9359 (mt) cc_final: 0.8869 (mt) REVERT: B 375 LYS cc_start: 0.8808 (mmmm) cc_final: 0.8452 (mmmm) REVERT: B 402 GLU cc_start: 0.8038 (mp0) cc_final: 0.7635 (mp0) REVERT: B 515 ASP cc_start: 0.8972 (m-30) cc_final: 0.8501 (p0) REVERT: B 546 LEU cc_start: 0.9460 (mm) cc_final: 0.9149 (mp) REVERT: B 558 TRP cc_start: 0.8775 (m100) cc_final: 0.8346 (m100) REVERT: B 586 TYR cc_start: 0.8986 (m-80) cc_final: 0.8582 (m-80) REVERT: B 634 MET cc_start: 0.8162 (mmp) cc_final: 0.7830 (mmt) REVERT: B 656 LEU cc_start: 0.9320 (mt) cc_final: 0.9027 (mt) REVERT: C 17 PHE cc_start: 0.8998 (p90) cc_final: 0.8520 (p90) REVERT: C 23 ASN cc_start: 0.9698 (m-40) cc_final: 0.9442 (m-40) REVERT: C 74 MET cc_start: 0.9415 (mpp) cc_final: 0.9045 (mpp) REVERT: C 154 PHE cc_start: 0.9244 (t80) cc_final: 0.8709 (t80) REVERT: C 157 MET cc_start: 0.9384 (mtm) cc_final: 0.8927 (ptt) REVERT: C 163 LEU cc_start: 0.9109 (tt) cc_final: 0.8811 (tp) REVERT: C 174 TYR cc_start: 0.8892 (t80) cc_final: 0.8545 (t80) REVERT: C 207 LEU cc_start: 0.9140 (mt) cc_final: 0.8868 (mt) REVERT: C 212 ILE cc_start: 0.8506 (OUTLIER) cc_final: 0.7873 (mm) REVERT: C 226 GLU cc_start: 0.8733 (tt0) cc_final: 0.8515 (tt0) REVERT: C 227 PHE cc_start: 0.8804 (t80) cc_final: 0.8587 (t80) REVERT: C 233 ASN cc_start: 0.9294 (m-40) cc_final: 0.8975 (m-40) REVERT: D 16 ASP cc_start: 0.6728 (t0) cc_final: 0.6446 (t0) REVERT: D 109 PHE cc_start: 0.8727 (m-10) cc_final: 0.8457 (m-80) REVERT: D 115 THR cc_start: 0.8471 (m) cc_final: 0.8249 (p) REVERT: D 119 ASN cc_start: 0.8533 (m110) cc_final: 0.8141 (m-40) REVERT: D 128 ASN cc_start: 0.8941 (t0) cc_final: 0.8086 (t0) REVERT: D 133 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7966 (tptp) REVERT: D 216 GLN cc_start: 0.7170 (mt0) cc_final: 0.6774 (mt0) REVERT: E 25 TRP cc_start: 0.8158 (p-90) cc_final: 0.7764 (p-90) REVERT: E 46 MET cc_start: 0.8048 (tpp) cc_final: 0.7035 (mpp) REVERT: E 70 MET cc_start: 0.8205 (mmp) cc_final: 0.7807 (mpp) outliers start: 6 outliers final: 1 residues processed: 734 average time/residue: 0.2804 time to fit residues: 306.1650 Evaluate side-chains 585 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 583 time to evaluate : 1.837 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 41 optimal weight: 0.0170 chunk 81 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 44 optimal weight: 4.9990 chunk 115 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 118 optimal weight: 6.9990 chunk 144 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 179 optimal weight: 10.0000 chunk 21 optimal weight: 5.9990 overall best weight: 1.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 19 GLN A 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN B 44 ASN B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.131285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.094250 restraints weight = 42136.484| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.097733 restraints weight = 22454.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.100043 restraints weight = 14263.105| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 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 = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7432 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 17041 Z= 0.179 Angle : 0.631 8.555 23026 Z= 0.329 Chirality : 0.044 0.390 2464 Planarity : 0.004 0.061 2931 Dihedral : 10.628 152.400 2325 Min Nonbonded Distance : 1.850 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.18 (0.18), residues: 2012 helix: 1.25 (0.15), residues: 1155 sheet: -0.18 (0.39), residues: 167 loop : 0.44 (0.24), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 623 HIS 0.008 0.001 HIS B 438 PHE 0.030 0.002 PHE C 166 TYR 0.027 0.002 TYR B 574 ARG 0.010 0.001 ARG A 669 Details of bonding type rmsd hydrogen bonds : bond 0.04346 ( 912) hydrogen bonds : angle 4.95505 ( 2664) SS BOND : bond 0.01330 ( 3) SS BOND : angle 3.88208 ( 6) covalent geometry : bond 0.00397 (17038) covalent geometry : angle 0.62806 (23020) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 710 time to evaluate : 2.018 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 60 GLU cc_start: 0.9174 (mp0) cc_final: 0.8947 (mm-30) REVERT: A 119 GLU cc_start: 0.8526 (mp0) cc_final: 0.8286 (mm-30) REVERT: A 162 LYS cc_start: 0.9361 (tmtt) cc_final: 0.9051 (tmmt) REVERT: A 195 LEU cc_start: 0.9381 (mt) cc_final: 0.9134 (mt) REVERT: A 209 LYS cc_start: 0.9082 (tttm) cc_final: 0.8832 (tttm) REVERT: A 254 PHE cc_start: 0.8871 (m-80) cc_final: 0.8358 (m-80) REVERT: A 266 LYS cc_start: 0.8925 (mtmm) cc_final: 0.8720 (mtmm) REVERT: A 286 ASP cc_start: 0.8779 (m-30) cc_final: 0.8447 (m-30) REVERT: A 301 PHE cc_start: 0.9067 (m-80) cc_final: 0.8850 (m-80) REVERT: A 362 ASP cc_start: 0.8554 (m-30) cc_final: 0.8262 (m-30) REVERT: A 367 VAL cc_start: 0.9538 (m) cc_final: 0.9267 (p) REVERT: A 390 GLN cc_start: 0.8664 (mt0) cc_final: 0.8292 (mt0) REVERT: A 417 LEU cc_start: 0.9396 (tp) cc_final: 0.9179 (tp) REVERT: A 421 GLU cc_start: 0.8344 (pp20) cc_final: 0.8006 (pp20) REVERT: A 639 ASP cc_start: 0.8834 (m-30) cc_final: 0.8549 (m-30) REVERT: A 658 LEU cc_start: 0.9598 (mp) cc_final: 0.9378 (mp) REVERT: A 686 ARG cc_start: 0.8071 (ttm-80) cc_final: 0.7290 (mtp85) REVERT: B 40 TYR cc_start: 0.9427 (t80) cc_final: 0.9088 (t80) REVERT: B 127 LEU cc_start: 0.9793 (mt) cc_final: 0.9515 (mm) REVERT: B 129 PHE cc_start: 0.9186 (m-80) cc_final: 0.8942 (m-80) REVERT: B 135 GLU cc_start: 0.8993 (mp0) cc_final: 0.8782 (pm20) REVERT: B 147 GLN cc_start: 0.9075 (mt0) cc_final: 0.8140 (mm-40) REVERT: B 150 GLN cc_start: 0.9365 (tp40) cc_final: 0.8870 (tp-100) REVERT: B 186 ILE cc_start: 0.9698 (mt) cc_final: 0.9193 (mt) REVERT: B 190 MET cc_start: 0.9363 (mtm) cc_final: 0.8969 (mtm) REVERT: B 232 ASN cc_start: 0.9146 (m-40) cc_final: 0.8914 (m110) REVERT: B 252 ASN cc_start: 0.9389 (t0) cc_final: 0.8991 (t0) REVERT: B 256 ARG cc_start: 0.8336 (tmt170) cc_final: 0.8042 (ttp80) REVERT: B 257 ASP cc_start: 0.8388 (m-30) cc_final: 0.7607 (m-30) REVERT: B 260 ASP cc_start: 0.9241 (m-30) cc_final: 0.8998 (p0) REVERT: B 286 ASP cc_start: 0.8407 (m-30) cc_final: 0.8158 (m-30) REVERT: B 307 TYR cc_start: 0.9299 (t80) cc_final: 0.9094 (t80) REVERT: B 317 MET cc_start: 0.8819 (mtp) cc_final: 0.8481 (mtt) REVERT: B 348 MET cc_start: 0.8960 (ppp) cc_final: 0.8456 (ppp) REVERT: B 349 LEU cc_start: 0.9341 (mt) cc_final: 0.8760 (mt) REVERT: B 361 GLN cc_start: 0.8621 (tt0) cc_final: 0.8249 (tp40) REVERT: B 375 LYS cc_start: 0.8845 (mmmm) cc_final: 0.8558 (mmmm) REVERT: B 402 GLU cc_start: 0.8149 (mp0) cc_final: 0.7795 (mp0) REVERT: B 415 ASN cc_start: 0.9116 (t0) cc_final: 0.8869 (t0) REVERT: B 437 THR cc_start: 0.9595 (m) cc_final: 0.9289 (m) REVERT: B 500 ILE cc_start: 0.9597 (tp) cc_final: 0.9287 (tp) REVERT: B 515 ASP cc_start: 0.8953 (m-30) cc_final: 0.8461 (p0) REVERT: B 526 GLU cc_start: 0.8907 (mp0) cc_final: 0.8664 (mp0) REVERT: B 558 TRP cc_start: 0.8893 (m100) cc_final: 0.8632 (m100) REVERT: B 570 MET cc_start: 0.8954 (mmm) cc_final: 0.8510 (tpt) REVERT: B 586 TYR cc_start: 0.9002 (m-80) cc_final: 0.8682 (m-80) REVERT: B 612 TYR cc_start: 0.8392 (m-80) cc_final: 0.7735 (m-80) REVERT: B 618 LEU cc_start: 0.8550 (tp) cc_final: 0.8216 (tp) REVERT: B 623 TRP cc_start: 0.8255 (t-100) cc_final: 0.7854 (t-100) REVERT: B 634 MET cc_start: 0.8212 (mmp) cc_final: 0.7918 (mmt) REVERT: B 650 GLN cc_start: 0.6911 (mt0) cc_final: 0.6437 (mt0) REVERT: B 656 LEU cc_start: 0.9346 (mt) cc_final: 0.9110 (mt) REVERT: C 17 PHE cc_start: 0.8966 (p90) cc_final: 0.8178 (p90) REVERT: C 20 MET cc_start: 0.9067 (ppp) cc_final: 0.8771 (ppp) REVERT: C 21 PHE cc_start: 0.8960 (m-80) cc_final: 0.8251 (m-80) REVERT: C 56 MET cc_start: 0.0819 (ptm) cc_final: 0.0320 (ttp) REVERT: C 74 MET cc_start: 0.9397 (mpp) cc_final: 0.9059 (mpp) REVERT: C 89 VAL cc_start: 0.7713 (t) cc_final: 0.7139 (m) REVERT: C 95 MET cc_start: 0.8590 (ttp) cc_final: 0.8115 (ttp) REVERT: C 157 MET cc_start: 0.9390 (mtm) cc_final: 0.8987 (ptp) REVERT: C 163 LEU cc_start: 0.9128 (tt) cc_final: 0.8777 (tp) REVERT: C 169 TYR cc_start: 0.8122 (m-80) cc_final: 0.7882 (m-80) REVERT: C 174 TYR cc_start: 0.9033 (t80) cc_final: 0.8379 (t80) REVERT: C 212 ILE cc_start: 0.8690 (mt) cc_final: 0.8338 (mm) REVERT: C 226 GLU cc_start: 0.8702 (tt0) cc_final: 0.8451 (tt0) REVERT: C 239 GLU cc_start: 0.9367 (pt0) cc_final: 0.9114 (pt0) REVERT: D 109 PHE cc_start: 0.8718 (m-10) cc_final: 0.8376 (m-80) REVERT: D 128 ASN cc_start: 0.8313 (t0) cc_final: 0.7775 (t0) REVERT: D 133 LYS cc_start: 0.8228 (ttmt) cc_final: 0.7849 (tptp) REVERT: D 313 GLU cc_start: 0.8272 (tt0) cc_final: 0.8024 (tm-30) REVERT: E 25 TRP cc_start: 0.8148 (p-90) cc_final: 0.7727 (p-90) REVERT: E 46 MET cc_start: 0.8136 (tpp) cc_final: 0.7897 (tpp) REVERT: E 70 MET cc_start: 0.8089 (mmp) cc_final: 0.7265 (mpp) outliers start: 1 outliers final: 0 residues processed: 710 average time/residue: 0.2820 time to fit residues: 302.2812 Evaluate side-chains 591 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 591 time to evaluate : 2.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 197 optimal weight: 20.0000 chunk 13 optimal weight: 7.9990 chunk 191 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 92 optimal weight: 6.9990 chunk 141 optimal weight: 20.0000 chunk 155 optimal weight: 3.9990 chunk 183 optimal weight: 7.9990 chunk 136 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 44 ASN A 320 ASN ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 645 GLN B 142 ASN B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 313 HIS ** B 370 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 475 ASN ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 650 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 192 ASN C 263 ASN C 270 ASN D 28 GLN ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.122750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.086891 restraints weight = 44014.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.090088 restraints weight = 23709.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.092211 restraints weight = 15110.702| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3168 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3168 r_free = 0.3168 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3167 r_free = 0.3167 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3167 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7674 moved from start: 0.6221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 17041 Z= 0.303 Angle : 0.738 9.928 23026 Z= 0.387 Chirality : 0.046 0.193 2464 Planarity : 0.004 0.044 2931 Dihedral : 10.832 154.201 2325 Min Nonbonded Distance : 1.685 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.11 % Allowed : 3.52 % Favored : 96.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.18), residues: 2012 helix: 0.80 (0.15), residues: 1182 sheet: -0.04 (0.39), residues: 157 loop : 0.14 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP A 623 HIS 0.007 0.002 HIS B 368 PHE 0.025 0.003 PHE B 491 TYR 0.026 0.002 TYR C 169 ARG 0.005 0.001 ARG A 274 Details of bonding type rmsd hydrogen bonds : bond 0.04585 ( 912) hydrogen bonds : angle 5.31705 ( 2664) SS BOND : bond 0.00708 ( 3) SS BOND : angle 4.16363 ( 6) covalent geometry : bond 0.00641 (17038) covalent geometry : angle 0.73498 (23020) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 661 time to evaluate : 1.806 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 101 TYR cc_start: 0.9310 (m-80) cc_final: 0.9073 (m-80) REVERT: A 119 GLU cc_start: 0.8813 (mp0) cc_final: 0.8565 (mm-30) REVERT: A 147 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8004 (tp-100) REVERT: A 195 LEU cc_start: 0.9415 (mt) cc_final: 0.9164 (mt) REVERT: A 243 ARG cc_start: 0.7213 (tpt-90) cc_final: 0.6990 (tpt-90) REVERT: A 250 TYR cc_start: 0.8223 (m-80) cc_final: 0.7949 (m-80) REVERT: A 257 ASP cc_start: 0.8860 (m-30) cc_final: 0.8459 (m-30) REVERT: A 266 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8723 (mtmm) REVERT: A 276 LYS cc_start: 0.8705 (mptt) cc_final: 0.8436 (tmtt) REVERT: A 290 GLU cc_start: 0.9119 (tm-30) cc_final: 0.8806 (tm-30) REVERT: A 291 LEU cc_start: 0.9528 (mm) cc_final: 0.9274 (mm) REVERT: A 301 PHE cc_start: 0.9014 (m-80) cc_final: 0.8698 (m-80) REVERT: A 322 MET cc_start: 0.7922 (mmm) cc_final: 0.7559 (mmm) REVERT: A 346 LEU cc_start: 0.9589 (mt) cc_final: 0.9367 (mt) REVERT: A 362 ASP cc_start: 0.8563 (m-30) cc_final: 0.8253 (m-30) REVERT: A 367 VAL cc_start: 0.9569 (m) cc_final: 0.9300 (p) REVERT: A 390 GLN cc_start: 0.8811 (mt0) cc_final: 0.8476 (mt0) REVERT: A 405 LEU cc_start: 0.8427 (mm) cc_final: 0.7654 (mm) REVERT: A 474 GLN cc_start: 0.8643 (tm-30) cc_final: 0.8187 (tm-30) REVERT: A 489 ASN cc_start: 0.8021 (t0) cc_final: 0.7722 (t0) REVERT: A 498 TYR cc_start: 0.8726 (m-80) cc_final: 0.8310 (m-80) REVERT: A 501 GLN cc_start: 0.9061 (tt0) cc_final: 0.8591 (tt0) REVERT: A 515 ASP cc_start: 0.8993 (m-30) cc_final: 0.8658 (m-30) REVERT: A 658 LEU cc_start: 0.9628 (mp) cc_final: 0.9310 (mp) REVERT: B 30 LYS cc_start: 0.9283 (tmtt) cc_final: 0.9035 (tptt) REVERT: B 51 LEU cc_start: 0.9343 (tp) cc_final: 0.9137 (tp) REVERT: B 66 GLU cc_start: 0.8252 (tp30) cc_final: 0.8024 (tp30) REVERT: B 87 LYS cc_start: 0.9193 (tppt) cc_final: 0.8641 (tptp) REVERT: B 129 PHE cc_start: 0.9155 (m-80) cc_final: 0.8935 (m-80) REVERT: B 147 GLN cc_start: 0.9280 (mt0) cc_final: 0.8797 (mt0) REVERT: B 184 ARG cc_start: 0.9381 (tpp80) cc_final: 0.8860 (tpp80) REVERT: B 256 ARG cc_start: 0.8373 (tmt170) cc_final: 0.8138 (ttp80) REVERT: B 257 ASP cc_start: 0.8352 (m-30) cc_final: 0.7262 (m-30) REVERT: B 258 ILE cc_start: 0.9408 (tp) cc_final: 0.9093 (tp) REVERT: B 317 MET cc_start: 0.8732 (mtp) cc_final: 0.8490 (mtt) REVERT: B 335 GLU cc_start: 0.7989 (tm-30) cc_final: 0.7770 (tm-30) REVERT: B 343 LEU cc_start: 0.9743 (mt) cc_final: 0.9501 (mm) REVERT: B 344 GLU cc_start: 0.9125 (pt0) cc_final: 0.8680 (pp20) REVERT: B 348 MET cc_start: 0.8912 (ppp) cc_final: 0.8436 (ppp) REVERT: B 349 LEU cc_start: 0.9380 (mt) cc_final: 0.8646 (mt) REVERT: B 402 GLU cc_start: 0.8256 (mp0) cc_final: 0.7637 (mp0) REVERT: B 415 ASN cc_start: 0.9189 (t0) cc_final: 0.8911 (t0) REVERT: B 427 LYS cc_start: 0.9195 (ptpp) cc_final: 0.8982 (ptpp) REVERT: B 437 THR cc_start: 0.9608 (m) cc_final: 0.9229 (m) REVERT: B 479 TYR cc_start: 0.8475 (t80) cc_final: 0.8167 (t80) REVERT: B 515 ASP cc_start: 0.8935 (m-30) cc_final: 0.8597 (p0) REVERT: B 526 GLU cc_start: 0.8913 (mp0) cc_final: 0.8611 (mp0) REVERT: B 570 MET cc_start: 0.9040 (mmm) cc_final: 0.8545 (mmm) REVERT: B 612 TYR cc_start: 0.8315 (m-80) cc_final: 0.7786 (m-80) REVERT: B 623 TRP cc_start: 0.8389 (t-100) cc_final: 0.7482 (t-100) REVERT: B 656 LEU cc_start: 0.9361 (mt) cc_final: 0.9110 (mt) REVERT: C 17 PHE cc_start: 0.9049 (p90) cc_final: 0.8343 (p90) REVERT: C 20 MET cc_start: 0.9250 (ppp) cc_final: 0.8981 (ppp) REVERT: C 21 PHE cc_start: 0.9071 (m-80) cc_final: 0.8342 (m-80) REVERT: C 56 MET cc_start: 0.1503 (ptm) cc_final: 0.0937 (ttp) REVERT: C 69 GLN cc_start: 0.9063 (tp40) cc_final: 0.8614 (tp-100) REVERT: C 95 MET cc_start: 0.8677 (ttp) cc_final: 0.7861 (ttp) REVERT: C 154 PHE cc_start: 0.9276 (t80) cc_final: 0.8908 (t80) REVERT: C 157 MET cc_start: 0.9446 (mtm) cc_final: 0.9041 (ptt) REVERT: C 163 LEU cc_start: 0.9294 (tt) cc_final: 0.8979 (tp) REVERT: C 174 TYR cc_start: 0.8997 (t80) cc_final: 0.8240 (t80) REVERT: C 187 SER cc_start: 0.8324 (m) cc_final: 0.7992 (p) REVERT: C 212 ILE cc_start: 0.8771 (OUTLIER) cc_final: 0.8317 (mm) REVERT: C 227 PHE cc_start: 0.8946 (t80) cc_final: 0.8641 (t80) REVERT: D 54 THR cc_start: 0.5703 (m) cc_final: 0.5466 (p) REVERT: D 133 LYS cc_start: 0.8392 (ttmt) cc_final: 0.8159 (tptp) REVERT: E 24 PHE cc_start: 0.8895 (m-80) cc_final: 0.8590 (m-80) REVERT: E 46 MET cc_start: 0.8336 (tpp) cc_final: 0.8025 (tpp) REVERT: E 60 ASN cc_start: 0.9439 (t0) cc_final: 0.9209 (t0) outliers start: 2 outliers final: 0 residues processed: 661 average time/residue: 0.2849 time to fit residues: 280.5611 Evaluate side-chains 557 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 556 time to evaluate : 1.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 132 optimal weight: 0.9990 chunk 124 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 144 optimal weight: 20.0000 chunk 48 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 123 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 86 optimal weight: 0.9980 chunk 154 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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 304 HIS A 365 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 438 HIS A 475 ASN A 645 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 218 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN B 313 HIS B 370 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 28 GLN ** C 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 136 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.133728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.095165 restraints weight = 42601.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.098841 restraints weight = 21700.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101276 restraints weight = 13498.807| |-----------------------------------------------------------------------------| r_work (final): 0.3249 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3256 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3256 r_free = 0.3256 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3256 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7530 moved from start: 0.6437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 17041 Z= 0.147 Angle : 0.630 9.720 23026 Z= 0.330 Chirality : 0.044 0.181 2464 Planarity : 0.004 0.043 2931 Dihedral : 10.480 145.762 2325 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 14.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 0.06 % Allowed : 1.57 % Favored : 98.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.19), residues: 2012 helix: 1.05 (0.15), residues: 1154 sheet: -0.18 (0.39), residues: 167 loop : 0.23 (0.24), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 124 HIS 0.008 0.001 HIS B 438 PHE 0.027 0.002 PHE D 109 TYR 0.035 0.002 TYR C 130 ARG 0.005 0.001 ARG A 161 Details of bonding type rmsd hydrogen bonds : bond 0.03982 ( 912) hydrogen bonds : angle 5.05799 ( 2664) SS BOND : bond 0.01347 ( 3) SS BOND : angle 5.03902 ( 6) covalent geometry : bond 0.00328 (17038) covalent geometry : angle 0.62478 (23020) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 694 time to evaluate : 1.936 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 8 LYS cc_start: 0.8928 (tptp) cc_final: 0.8590 (tppt) REVERT: A 89 PHE cc_start: 0.9165 (t80) cc_final: 0.8904 (t80) REVERT: A 119 GLU cc_start: 0.8570 (mp0) cc_final: 0.8274 (mm-30) REVERT: A 147 GLN cc_start: 0.8644 (tp-100) cc_final: 0.7395 (tp40) REVERT: A 162 LYS cc_start: 0.9366 (tmtt) cc_final: 0.9165 (tmmt) REVERT: A 187 ASP cc_start: 0.8616 (t70) cc_final: 0.8228 (t0) REVERT: A 250 TYR cc_start: 0.8206 (m-80) cc_final: 0.7857 (m-80) REVERT: A 254 PHE cc_start: 0.8966 (m-80) cc_final: 0.8744 (m-80) REVERT: A 290 GLU cc_start: 0.9094 (tm-30) cc_final: 0.8660 (tm-30) REVERT: A 291 LEU cc_start: 0.9525 (mm) cc_final: 0.9057 (mm) REVERT: A 301 PHE cc_start: 0.8973 (m-80) cc_final: 0.8743 (m-80) REVERT: A 346 LEU cc_start: 0.9527 (mt) cc_final: 0.9318 (mt) REVERT: A 362 ASP cc_start: 0.8415 (m-30) cc_final: 0.7716 (m-30) REVERT: A 367 VAL cc_start: 0.9542 (m) cc_final: 0.9289 (p) REVERT: A 390 GLN cc_start: 0.8763 (mt0) cc_final: 0.8479 (mt0) REVERT: A 418 ASN cc_start: 0.9377 (m-40) cc_final: 0.8761 (m110) REVERT: A 494 MET cc_start: 0.8491 (mmp) cc_final: 0.8235 (mmp) REVERT: A 498 TYR cc_start: 0.8719 (m-80) cc_final: 0.8422 (m-80) REVERT: A 515 ASP cc_start: 0.8992 (m-30) cc_final: 0.8552 (m-30) REVERT: A 645 GLN cc_start: 0.8736 (tp40) cc_final: 0.8268 (tp-100) REVERT: A 658 LEU cc_start: 0.9553 (mp) cc_final: 0.9327 (mp) REVERT: A 686 ARG cc_start: 0.8185 (ttm-80) cc_final: 0.7957 (mtp85) REVERT: B 16 ILE cc_start: 0.9309 (tp) cc_final: 0.9068 (tp) REVERT: B 18 ILE cc_start: 0.9394 (mm) cc_final: 0.9021 (pt) REVERT: B 30 LYS cc_start: 0.9295 (tmtt) cc_final: 0.9093 (tptt) REVERT: B 66 GLU cc_start: 0.8383 (tp30) cc_final: 0.8028 (tp30) REVERT: B 87 LYS cc_start: 0.9174 (tppt) cc_final: 0.8576 (tptp) REVERT: B 129 PHE cc_start: 0.9161 (m-80) cc_final: 0.8879 (m-80) REVERT: B 147 GLN cc_start: 0.9185 (mt0) cc_final: 0.8224 (mt0) REVERT: B 184 ARG cc_start: 0.9340 (tpp80) cc_final: 0.8684 (tpp80) REVERT: B 186 ILE cc_start: 0.9566 (mt) cc_final: 0.9293 (mt) REVERT: B 190 MET cc_start: 0.9335 (mtm) cc_final: 0.8799 (mtm) REVERT: B 256 ARG cc_start: 0.8328 (tmt170) cc_final: 0.8033 (ttp80) REVERT: B 257 ASP cc_start: 0.8219 (m-30) cc_final: 0.7535 (m-30) REVERT: B 286 ASP cc_start: 0.8446 (m-30) cc_final: 0.8015 (m-30) REVERT: B 335 GLU cc_start: 0.7979 (tm-30) cc_final: 0.7675 (tm-30) REVERT: B 348 MET cc_start: 0.9014 (ppp) cc_final: 0.8491 (ppp) REVERT: B 349 LEU cc_start: 0.9375 (mt) cc_final: 0.8655 (mt) REVERT: B 358 ILE cc_start: 0.9617 (mm) cc_final: 0.9389 (mm) REVERT: B 370 ASN cc_start: 0.9533 (m-40) cc_final: 0.9094 (m110) REVERT: B 402 GLU cc_start: 0.8204 (mp0) cc_final: 0.7519 (mp0) REVERT: B 415 ASN cc_start: 0.9048 (t0) cc_final: 0.8822 (t0) REVERT: B 427 LYS cc_start: 0.9166 (ptpp) cc_final: 0.8881 (ptpp) REVERT: B 437 THR cc_start: 0.9578 (m) cc_final: 0.9223 (m) REVERT: B 446 ARG cc_start: 0.7754 (mmt-90) cc_final: 0.7207 (mpt90) REVERT: B 493 MET cc_start: 0.9338 (tmm) cc_final: 0.8584 (tmm) REVERT: B 526 GLU cc_start: 0.8926 (mp0) cc_final: 0.8659 (mp0) REVERT: B 570 MET cc_start: 0.8985 (mmm) cc_final: 0.8519 (tpp) REVERT: B 612 TYR cc_start: 0.8382 (m-80) cc_final: 0.7992 (m-80) REVERT: B 632 MET cc_start: 0.8196 (mtp) cc_final: 0.7924 (mtp) REVERT: B 656 LEU cc_start: 0.9324 (mt) cc_final: 0.9066 (mt) REVERT: C 17 PHE cc_start: 0.9015 (p90) cc_final: 0.8314 (p90) REVERT: C 20 MET cc_start: 0.9309 (ppp) cc_final: 0.9078 (ppp) REVERT: C 21 PHE cc_start: 0.8982 (m-80) cc_final: 0.8394 (m-80) REVERT: C 46 TYR cc_start: 0.8575 (m-80) cc_final: 0.8021 (m-80) REVERT: C 56 MET cc_start: 0.1181 (ptm) cc_final: 0.0575 (ttp) REVERT: C 74 MET cc_start: 0.9356 (mpp) cc_final: 0.8976 (mpp) REVERT: C 89 VAL cc_start: 0.6813 (m) cc_final: 0.6381 (t) REVERT: C 95 MET cc_start: 0.8582 (ttp) cc_final: 0.7882 (ttp) REVERT: C 137 MET cc_start: 0.8449 (mmm) cc_final: 0.8237 (mmt) REVERT: C 154 PHE cc_start: 0.9231 (t80) cc_final: 0.8939 (t80) REVERT: C 157 MET cc_start: 0.9411 (mtm) cc_final: 0.9058 (ptt) REVERT: C 163 LEU cc_start: 0.9259 (tt) cc_final: 0.8852 (tt) REVERT: C 169 TYR cc_start: 0.8310 (m-10) cc_final: 0.8099 (m-80) REVERT: C 174 TYR cc_start: 0.9006 (t80) cc_final: 0.8225 (t80) REVERT: C 212 ILE cc_start: 0.8669 (mt) cc_final: 0.8344 (mm) REVERT: C 231 LEU cc_start: 0.9153 (mt) cc_final: 0.8937 (mt) REVERT: D 96 MET cc_start: 0.7939 (tpt) cc_final: 0.7443 (tpt) REVERT: D 128 ASN cc_start: 0.8344 (t0) cc_final: 0.7964 (t0) REVERT: D 133 LYS cc_start: 0.8612 (ttmt) cc_final: 0.8176 (tptp) REVERT: D 185 MET cc_start: 0.6640 (ptm) cc_final: 0.6400 (ptm) REVERT: E 24 PHE cc_start: 0.8850 (m-80) cc_final: 0.8595 (m-80) REVERT: E 25 TRP cc_start: 0.8027 (p-90) cc_final: 0.7430 (p-90) REVERT: E 46 MET cc_start: 0.8322 (tpp) cc_final: 0.8033 (tpp) REVERT: E 60 ASN cc_start: 0.9402 (t0) cc_final: 0.9183 (t0) outliers start: 1 outliers final: 0 residues processed: 694 average time/residue: 0.2701 time to fit residues: 282.0399 Evaluate side-chains 559 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 559 time to evaluate : 1.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 14 optimal weight: 0.6980 chunk 69 optimal weight: 2.9990 chunk 119 optimal weight: 7.9990 chunk 170 optimal weight: 9.9990 chunk 186 optimal weight: 20.0000 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 77 optimal weight: 0.9990 chunk 135 optimal weight: 5.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 158 ASN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 150 GLN B 191 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 668 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN C 210 GLN C 234 GLN C 238 ASN C 270 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.130341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.091937 restraints weight = 42932.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.095597 restraints weight = 22335.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.098033 restraints weight = 13882.633| |-----------------------------------------------------------------------------| r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3253 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3253 r_free = 0.3253 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3253 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7575 moved from start: 0.6668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 17041 Z= 0.153 Angle : 0.627 8.999 23026 Z= 0.328 Chirality : 0.043 0.207 2464 Planarity : 0.004 0.046 2931 Dihedral : 10.339 144.865 2325 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 14.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.11 % Allowed : 1.96 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.18), residues: 2012 helix: 1.01 (0.15), residues: 1149 sheet: -0.12 (0.40), residues: 157 loop : 0.20 (0.24), residues: 706 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 623 HIS 0.006 0.001 HIS C 201 PHE 0.037 0.002 PHE B 171 TYR 0.025 0.002 TYR D 105 ARG 0.004 0.001 ARG B 452 Details of bonding type rmsd hydrogen bonds : bond 0.03887 ( 912) hydrogen bonds : angle 4.98435 ( 2664) SS BOND : bond 0.00572 ( 3) SS BOND : angle 3.96253 ( 6) covalent geometry : bond 0.00342 (17038) covalent geometry : angle 0.62338 (23020) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 671 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 669 time to evaluate : 1.871 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: A 119 GLU cc_start: 0.8539 (mp0) cc_final: 0.8284 (mm-30) REVERT: A 147 GLN cc_start: 0.8609 (tp-100) cc_final: 0.8298 (tp40) REVERT: A 150 GLN cc_start: 0.8677 (tp40) cc_final: 0.8194 (tp40) REVERT: A 162 LYS cc_start: 0.9298 (tmtt) cc_final: 0.8958 (ttpt) REVERT: A 223 VAL cc_start: 0.9256 (p) cc_final: 0.8938 (p) REVERT: A 230 LEU cc_start: 0.9697 (mt) cc_final: 0.9471 (mt) REVERT: A 234 PHE cc_start: 0.9503 (m-80) cc_final: 0.9238 (m-80) REVERT: A 250 TYR cc_start: 0.8296 (m-80) cc_final: 0.8052 (m-80) REVERT: A 254 PHE cc_start: 0.8883 (m-80) cc_final: 0.8505 (m-80) REVERT: A 286 ASP cc_start: 0.8832 (m-30) cc_final: 0.8631 (m-30) REVERT: A 290 GLU cc_start: 0.9095 (tm-30) cc_final: 0.8653 (tm-30) REVERT: A 291 LEU cc_start: 0.9531 (mm) cc_final: 0.9049 (mm) REVERT: A 301 PHE cc_start: 0.9071 (m-80) cc_final: 0.8755 (m-80) REVERT: A 312 GLN cc_start: 0.8589 (tp-100) cc_final: 0.8119 (tp40) REVERT: A 338 ASN cc_start: 0.9520 (t0) cc_final: 0.9147 (t0) REVERT: A 346 LEU cc_start: 0.9508 (mt) cc_final: 0.9298 (mt) REVERT: A 358 ILE cc_start: 0.9228 (mm) cc_final: 0.8983 (mm) REVERT: A 362 ASP cc_start: 0.8365 (m-30) cc_final: 0.7613 (m-30) REVERT: A 367 VAL cc_start: 0.9553 (m) cc_final: 0.9333 (p) REVERT: A 479 TYR cc_start: 0.8812 (t80) cc_final: 0.8547 (t80) REVERT: A 491 PHE cc_start: 0.9493 (t80) cc_final: 0.9024 (t80) REVERT: A 498 TYR cc_start: 0.8756 (m-80) cc_final: 0.8441 (m-80) REVERT: A 501 GLN cc_start: 0.9031 (tt0) cc_final: 0.8542 (tt0) REVERT: A 515 ASP cc_start: 0.8972 (m-30) cc_final: 0.8648 (m-30) REVERT: A 529 ASP cc_start: 0.9142 (p0) cc_final: 0.8926 (p0) REVERT: A 645 GLN cc_start: 0.8752 (tp40) cc_final: 0.8379 (tp40) REVERT: A 669 ARG cc_start: 0.9031 (mmm160) cc_final: 0.8551 (mmt180) REVERT: B 9 TRP cc_start: 0.9486 (p90) cc_final: 0.8995 (p90) REVERT: B 18 ILE cc_start: 0.9487 (mm) cc_final: 0.9259 (tp) REVERT: B 30 LYS cc_start: 0.9276 (tmtt) cc_final: 0.9055 (tptt) REVERT: B 66 GLU cc_start: 0.8300 (tp30) cc_final: 0.7929 (tp30) REVERT: B 87 LYS cc_start: 0.9142 (tppt) cc_final: 0.8593 (tptp) REVERT: B 117 ARG cc_start: 0.8009 (mmm160) cc_final: 0.7707 (mmm-85) REVERT: B 120 ASP cc_start: 0.8753 (m-30) cc_final: 0.8306 (m-30) REVERT: B 129 PHE cc_start: 0.9122 (m-10) cc_final: 0.8869 (m-80) REVERT: B 147 GLN cc_start: 0.9194 (mt0) cc_final: 0.8257 (mt0) REVERT: B 186 ILE cc_start: 0.9579 (mt) cc_final: 0.9304 (mt) REVERT: B 190 MET cc_start: 0.9312 (mtm) cc_final: 0.8866 (mtm) REVERT: B 228 LYS cc_start: 0.9552 (mmmt) cc_final: 0.9200 (mmmt) REVERT: B 257 ASP cc_start: 0.8494 (m-30) cc_final: 0.7703 (m-30) REVERT: B 286 ASP cc_start: 0.8549 (m-30) cc_final: 0.8093 (m-30) REVERT: B 335 GLU cc_start: 0.7909 (tm-30) cc_final: 0.7671 (tm-30) REVERT: B 348 MET cc_start: 0.8985 (ppp) cc_final: 0.8482 (ppp) REVERT: B 349 LEU cc_start: 0.9329 (mt) cc_final: 0.8584 (mt) REVERT: B 358 ILE cc_start: 0.9572 (mm) cc_final: 0.9274 (mm) REVERT: B 370 ASN cc_start: 0.9536 (m-40) cc_final: 0.9207 (m110) REVERT: B 378 PHE cc_start: 0.8851 (p90) cc_final: 0.8405 (p90) REVERT: B 402 GLU cc_start: 0.8249 (mp0) cc_final: 0.7574 (mp0) REVERT: B 437 THR cc_start: 0.9572 (m) cc_final: 0.9204 (m) REVERT: B 493 MET cc_start: 0.9277 (tmm) cc_final: 0.8598 (tmm) REVERT: B 526 GLU cc_start: 0.8922 (mp0) cc_final: 0.8709 (mp0) REVERT: B 570 MET cc_start: 0.8958 (mmm) cc_final: 0.8599 (tpp) REVERT: B 612 TYR cc_start: 0.8380 (m-80) cc_final: 0.7451 (m-80) REVERT: B 623 TRP cc_start: 0.8830 (t-100) cc_final: 0.8549 (t-100) REVERT: B 656 LEU cc_start: 0.9319 (mt) cc_final: 0.9098 (mt) REVERT: C 17 PHE cc_start: 0.9038 (p90) cc_final: 0.8278 (p90) REVERT: C 20 MET cc_start: 0.9306 (ppp) cc_final: 0.9076 (ppp) REVERT: C 21 PHE cc_start: 0.8987 (m-80) cc_final: 0.8405 (m-80) REVERT: C 46 TYR cc_start: 0.8174 (m-80) cc_final: 0.7909 (m-80) REVERT: C 56 MET cc_start: 0.1032 (ptm) cc_final: 0.0461 (ttp) REVERT: C 74 MET cc_start: 0.9275 (mpp) cc_final: 0.8993 (mpp) REVERT: C 89 VAL cc_start: 0.6977 (m) cc_final: 0.6599 (t) REVERT: C 95 MET cc_start: 0.8565 (ttp) cc_final: 0.7971 (ttp) REVERT: C 137 MET cc_start: 0.8638 (mmm) cc_final: 0.8435 (mmt) REVERT: C 163 LEU cc_start: 0.9268 (tt) cc_final: 0.9023 (tt) REVERT: C 174 TYR cc_start: 0.8949 (t80) cc_final: 0.8279 (t80) REVERT: C 212 ILE cc_start: 0.8734 (mt) cc_final: 0.8388 (mm) REVERT: C 231 LEU cc_start: 0.9134 (mt) cc_final: 0.8820 (pp) REVERT: C 239 GLU cc_start: 0.9063 (pt0) cc_final: 0.8599 (pt0) REVERT: C 274 ASP cc_start: 0.9058 (p0) cc_final: 0.8817 (p0) REVERT: C 320 PHE cc_start: 0.9137 (m-80) cc_final: 0.8897 (m-80) REVERT: D 96 MET cc_start: 0.7972 (tpt) cc_final: 0.7632 (tpt) REVERT: D 109 PHE cc_start: 0.8559 (m-80) cc_final: 0.8339 (m-80) REVERT: D 133 LYS cc_start: 0.8593 (ttmt) cc_final: 0.8177 (tptp) REVERT: D 185 MET cc_start: 0.6530 (ptm) cc_final: 0.6260 (ptm) REVERT: D 238 ASN cc_start: 0.8444 (m110) cc_final: 0.7575 (m110) REVERT: E 24 PHE cc_start: 0.8945 (m-80) cc_final: 0.8679 (m-80) REVERT: E 25 TRP cc_start: 0.8072 (p-90) cc_final: 0.7403 (p-90) REVERT: E 46 MET cc_start: 0.8324 (tpp) cc_final: 0.8038 (tpp) REVERT: E 60 ASN cc_start: 0.9407 (t0) cc_final: 0.9166 (t0) outliers start: 2 outliers final: 2 residues processed: 671 average time/residue: 0.2816 time to fit residues: 280.8636 Evaluate side-chains 555 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 553 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 32 optimal weight: 4.9990 chunk 36 optimal weight: 5.9990 chunk 61 optimal weight: 10.0000 chunk 149 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 137 optimal weight: 8.9990 chunk 141 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 97 optimal weight: 0.1980 chunk 132 optimal weight: 0.8980 overall best weight: 2.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 28 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 132 GLN ** D 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.131842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.094197 restraints weight = 43023.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.097793 restraints weight = 22186.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.100163 restraints weight = 13823.763| |-----------------------------------------------------------------------------| r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3231 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3231 r_free = 0.3231 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3231 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7614 moved from start: 0.6918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.095 17041 Z= 0.183 Angle : 0.662 10.473 23026 Z= 0.344 Chirality : 0.044 0.202 2464 Planarity : 0.004 0.043 2931 Dihedral : 10.266 142.566 2325 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.18), residues: 2012 helix: 0.98 (0.15), residues: 1160 sheet: -0.24 (0.39), residues: 165 loop : 0.11 (0.24), residues: 687 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 623 HIS 0.007 0.001 HIS B 255 PHE 0.031 0.002 PHE D 122 TYR 0.026 0.002 TYR D 105 ARG 0.007 0.001 ARG D 196 Details of bonding type rmsd hydrogen bonds : bond 0.03914 ( 912) hydrogen bonds : angle 5.11685 ( 2664) SS BOND : bond 0.00370 ( 3) SS BOND : angle 4.95154 ( 6) covalent geometry : bond 0.00405 (17038) covalent geometry : angle 0.65682 (23020) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 651 time to evaluate : 1.729 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 8 LYS cc_start: 0.9063 (tptp) cc_final: 0.8573 (tppt) REVERT: A 12 LEU cc_start: 0.9610 (mt) cc_final: 0.9338 (mt) REVERT: A 119 GLU cc_start: 0.8636 (mp0) cc_final: 0.8383 (mm-30) REVERT: A 147 GLN cc_start: 0.8753 (tp-100) cc_final: 0.8467 (tp40) REVERT: A 150 GLN cc_start: 0.8672 (tp40) cc_final: 0.8305 (tp40) REVERT: A 230 LEU cc_start: 0.9700 (mt) cc_final: 0.9492 (mt) REVERT: A 250 TYR cc_start: 0.8239 (m-80) cc_final: 0.7911 (m-80) REVERT: A 254 PHE cc_start: 0.8930 (m-80) cc_final: 0.8508 (m-80) REVERT: A 290 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8608 (tm-30) REVERT: A 291 LEU cc_start: 0.9513 (mm) cc_final: 0.9075 (mm) REVERT: A 301 PHE cc_start: 0.9043 (m-80) cc_final: 0.8697 (m-80) REVERT: A 338 ASN cc_start: 0.9311 (t0) cc_final: 0.8089 (t0) REVERT: A 358 ILE cc_start: 0.9178 (mm) cc_final: 0.8897 (mm) REVERT: A 362 ASP cc_start: 0.8496 (m-30) cc_final: 0.7686 (m-30) REVERT: A 367 VAL cc_start: 0.9544 (m) cc_final: 0.9317 (p) REVERT: A 390 GLN cc_start: 0.8821 (mt0) cc_final: 0.8617 (mt0) REVERT: A 425 ILE cc_start: 0.8746 (mp) cc_final: 0.8520 (tp) REVERT: A 469 HIS cc_start: 0.8174 (t-170) cc_final: 0.7775 (t-170) REVERT: A 474 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8295 (tm-30) REVERT: A 479 TYR cc_start: 0.8732 (t80) cc_final: 0.8477 (t80) REVERT: A 491 PHE cc_start: 0.9510 (t80) cc_final: 0.9185 (t80) REVERT: A 493 MET cc_start: 0.8012 (tmm) cc_final: 0.7694 (tmm) REVERT: A 498 TYR cc_start: 0.8783 (m-80) cc_final: 0.8390 (m-80) REVERT: A 501 GLN cc_start: 0.9044 (tt0) cc_final: 0.8499 (tm-30) REVERT: A 515 ASP cc_start: 0.8926 (m-30) cc_final: 0.8557 (m-30) REVERT: A 590 SER cc_start: 0.9525 (t) cc_final: 0.8892 (p) REVERT: A 645 GLN cc_start: 0.8727 (tp40) cc_final: 0.8470 (tp-100) REVERT: A 647 HIS cc_start: 0.8639 (m-70) cc_final: 0.8331 (m90) REVERT: A 669 ARG cc_start: 0.9040 (mmm160) cc_final: 0.8482 (mmt180) REVERT: B 28 LYS cc_start: 0.9283 (mmtp) cc_final: 0.8637 (mmmm) REVERT: B 66 GLU cc_start: 0.8382 (tp30) cc_final: 0.8072 (tp30) REVERT: B 87 LYS cc_start: 0.9161 (tppt) cc_final: 0.8620 (tptp) REVERT: B 100 PHE cc_start: 0.9108 (t80) cc_final: 0.8851 (t80) REVERT: B 120 ASP cc_start: 0.8803 (m-30) cc_final: 0.8596 (m-30) REVERT: B 129 PHE cc_start: 0.9136 (m-10) cc_final: 0.8887 (m-80) REVERT: B 147 GLN cc_start: 0.9239 (mt0) cc_final: 0.8334 (mt0) REVERT: B 186 ILE cc_start: 0.9553 (mt) cc_final: 0.9243 (mt) REVERT: B 190 MET cc_start: 0.9272 (mtm) cc_final: 0.8829 (mtm) REVERT: B 202 ASN cc_start: 0.8706 (t0) cc_final: 0.8025 (t0) REVERT: B 258 ILE cc_start: 0.9450 (tp) cc_final: 0.9201 (tp) REVERT: B 286 ASP cc_start: 0.8617 (m-30) cc_final: 0.8000 (m-30) REVERT: B 348 MET cc_start: 0.8949 (ppp) cc_final: 0.8417 (ppp) REVERT: B 349 LEU cc_start: 0.9349 (mt) cc_final: 0.8607 (mt) REVERT: B 358 ILE cc_start: 0.9600 (mm) cc_final: 0.9380 (mm) REVERT: B 370 ASN cc_start: 0.9560 (m-40) cc_final: 0.9321 (m110) REVERT: B 378 PHE cc_start: 0.8955 (p90) cc_final: 0.8420 (p90) REVERT: B 402 GLU cc_start: 0.8294 (mp0) cc_final: 0.7600 (mp0) REVERT: B 427 LYS cc_start: 0.9160 (ptpp) cc_final: 0.8909 (ptpp) REVERT: B 437 THR cc_start: 0.9589 (m) cc_final: 0.9221 (m) REVERT: B 493 MET cc_start: 0.9245 (tmm) cc_final: 0.8597 (tmm) REVERT: B 526 GLU cc_start: 0.8946 (mp0) cc_final: 0.8719 (mp0) REVERT: B 570 MET cc_start: 0.8916 (mmm) cc_final: 0.8427 (tpt) REVERT: B 612 TYR cc_start: 0.8296 (m-80) cc_final: 0.7691 (m-80) REVERT: B 623 TRP cc_start: 0.8929 (t-100) cc_final: 0.8602 (t-100) REVERT: B 656 LEU cc_start: 0.9300 (mt) cc_final: 0.9062 (mt) REVERT: C 17 PHE cc_start: 0.9004 (p90) cc_final: 0.8304 (p90) REVERT: C 20 MET cc_start: 0.9358 (ppp) cc_final: 0.9145 (ppp) REVERT: C 21 PHE cc_start: 0.9059 (m-80) cc_final: 0.8485 (m-80) REVERT: C 56 MET cc_start: 0.1251 (ptm) cc_final: 0.0668 (ttp) REVERT: C 74 MET cc_start: 0.9305 (mpp) cc_final: 0.9072 (mpp) REVERT: C 89 VAL cc_start: 0.7148 (m) cc_final: 0.6705 (m) REVERT: C 95 MET cc_start: 0.8549 (ttp) cc_final: 0.7998 (ttp) REVERT: C 137 MET cc_start: 0.8742 (mmm) cc_final: 0.8508 (mmt) REVERT: C 163 LEU cc_start: 0.9326 (tt) cc_final: 0.9076 (tt) REVERT: C 174 TYR cc_start: 0.8944 (t80) cc_final: 0.8122 (t80) REVERT: C 212 ILE cc_start: 0.8897 (mt) cc_final: 0.8631 (tp) REVERT: C 231 LEU cc_start: 0.9221 (mt) cc_final: 0.8907 (pp) REVERT: C 239 GLU cc_start: 0.8978 (pt0) cc_final: 0.8511 (pt0) REVERT: C 274 ASP cc_start: 0.9043 (p0) cc_final: 0.8816 (p0) REVERT: D 25 ASN cc_start: 0.9474 (m-40) cc_final: 0.9266 (m-40) REVERT: D 128 ASN cc_start: 0.8437 (t0) cc_final: 0.8115 (t0) REVERT: D 137 MET cc_start: 0.8395 (mmp) cc_final: 0.7897 (mtt) REVERT: D 185 MET cc_start: 0.6460 (ptm) cc_final: 0.6131 (ptm) REVERT: E 24 PHE cc_start: 0.8993 (m-80) cc_final: 0.8689 (m-80) REVERT: E 25 TRP cc_start: 0.8003 (p-90) cc_final: 0.7408 (p-90) REVERT: E 46 MET cc_start: 0.8293 (tpp) cc_final: 0.8012 (tpp) REVERT: E 60 ASN cc_start: 0.9345 (t0) cc_final: 0.9078 (t0) REVERT: E 85 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7630 (tm-30) outliers start: 0 outliers final: 0 residues processed: 651 average time/residue: 0.2742 time to fit residues: 267.4383 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 : 1.905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 73 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 139 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 55 optimal weight: 8.9990 chunk 158 optimal weight: 10.0000 chunk 194 optimal weight: 7.9990 chunk 67 optimal weight: 2.9990 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 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 418 ASN ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 238 ASN ** D 28 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.097458 restraints weight = 43093.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100942 restraints weight = 22570.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.103213 restraints weight = 14107.339| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3274 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3274 r_free = 0.3274 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3274 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 17041 Z= 0.152 Angle : 0.649 9.265 23026 Z= 0.335 Chirality : 0.044 0.265 2464 Planarity : 0.004 0.049 2931 Dihedral : 10.085 141.837 2325 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.18), residues: 2012 helix: 0.93 (0.15), residues: 1163 sheet: -0.14 (0.40), residues: 157 loop : 0.09 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 623 HIS 0.007 0.001 HIS C 201 PHE 0.036 0.002 PHE A 234 TYR 0.025 0.002 TYR D 105 ARG 0.007 0.001 ARG B 485 Details of bonding type rmsd hydrogen bonds : bond 0.03816 ( 912) hydrogen bonds : angle 4.99850 ( 2664) SS BOND : bond 0.00488 ( 3) SS BOND : angle 4.19748 ( 6) covalent geometry : bond 0.00343 (17038) covalent geometry : angle 0.64570 (23020) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 653 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 653 time to evaluate : 1.808 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 8 LYS cc_start: 0.9046 (tptp) cc_final: 0.8577 (tppt) REVERT: A 12 LEU cc_start: 0.9571 (mt) cc_final: 0.9303 (mt) REVERT: A 119 GLU cc_start: 0.8612 (mp0) cc_final: 0.8347 (mm-30) REVERT: A 150 GLN cc_start: 0.8566 (tp40) cc_final: 0.8180 (tp40) REVERT: A 162 LYS cc_start: 0.9342 (tmtt) cc_final: 0.9060 (ttpt) REVERT: A 223 VAL cc_start: 0.9282 (p) cc_final: 0.8952 (p) REVERT: A 250 TYR cc_start: 0.8314 (m-80) cc_final: 0.8015 (m-80) REVERT: A 252 ASN cc_start: 0.9445 (t0) cc_final: 0.9229 (t0) REVERT: A 254 PHE cc_start: 0.8879 (m-80) cc_final: 0.8472 (m-80) REVERT: A 290 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8571 (tm-30) REVERT: A 291 LEU cc_start: 0.9496 (mm) cc_final: 0.9023 (mm) REVERT: A 301 PHE cc_start: 0.9026 (m-80) cc_final: 0.8594 (m-80) REVERT: A 362 ASP cc_start: 0.8407 (m-30) cc_final: 0.7724 (m-30) REVERT: A 390 GLN cc_start: 0.8783 (mt0) cc_final: 0.8570 (mt0) REVERT: A 469 HIS cc_start: 0.8214 (t-170) cc_final: 0.7971 (t-90) REVERT: A 474 GLN cc_start: 0.8773 (tm-30) cc_final: 0.8274 (tm-30) REVERT: A 479 TYR cc_start: 0.8719 (t80) cc_final: 0.8248 (t80) REVERT: A 491 PHE cc_start: 0.9401 (t80) cc_final: 0.9059 (t80) REVERT: A 494 MET cc_start: 0.8419 (mmt) cc_final: 0.8153 (mmt) REVERT: A 498 TYR cc_start: 0.8773 (m-80) cc_final: 0.8417 (m-80) REVERT: A 501 GLN cc_start: 0.9021 (tt0) cc_final: 0.8480 (tm-30) REVERT: A 515 ASP cc_start: 0.8857 (m-30) cc_final: 0.8454 (m-30) REVERT: A 590 SER cc_start: 0.9514 (t) cc_final: 0.9208 (p) REVERT: A 647 HIS cc_start: 0.8562 (m-70) cc_final: 0.8212 (m90) REVERT: A 669 ARG cc_start: 0.9040 (mmm160) cc_final: 0.8488 (mmt180) REVERT: B 30 LYS cc_start: 0.9213 (tmtt) cc_final: 0.8999 (tptt) REVERT: B 66 GLU cc_start: 0.8340 (tp30) cc_final: 0.7917 (tp30) REVERT: B 87 LYS cc_start: 0.9103 (tppt) cc_final: 0.8601 (tptp) REVERT: B 112 LYS cc_start: 0.9427 (mmpt) cc_final: 0.9227 (mmmt) REVERT: B 120 ASP cc_start: 0.8828 (m-30) cc_final: 0.8606 (m-30) REVERT: B 129 PHE cc_start: 0.9087 (m-10) cc_final: 0.8825 (m-80) REVERT: B 147 GLN cc_start: 0.9187 (mt0) cc_final: 0.8344 (mt0) REVERT: B 150 GLN cc_start: 0.9514 (tp40) cc_final: 0.9304 (tp40) REVERT: B 186 ILE cc_start: 0.9555 (mt) cc_final: 0.9299 (mt) REVERT: B 190 MET cc_start: 0.9272 (mtm) cc_final: 0.8831 (mtm) REVERT: B 227 MET cc_start: 0.8990 (mtm) cc_final: 0.8777 (mtm) REVERT: B 228 LYS cc_start: 0.9517 (mmmt) cc_final: 0.9187 (mmmt) REVERT: B 286 ASP cc_start: 0.8425 (m-30) cc_final: 0.7816 (m-30) REVERT: B 335 GLU cc_start: 0.7871 (tm-30) cc_final: 0.7667 (tm-30) REVERT: B 348 MET cc_start: 0.8976 (ppp) cc_final: 0.8417 (ppp) REVERT: B 349 LEU cc_start: 0.9316 (mt) cc_final: 0.8590 (mt) REVERT: B 370 ASN cc_start: 0.9528 (m-40) cc_final: 0.9170 (m110) REVERT: B 378 PHE cc_start: 0.8944 (p90) cc_final: 0.8506 (p90) REVERT: B 402 GLU cc_start: 0.8288 (mp0) cc_final: 0.7620 (mp0) REVERT: B 427 LYS cc_start: 0.9147 (ptpp) cc_final: 0.8942 (ptpp) REVERT: B 437 THR cc_start: 0.9574 (m) cc_final: 0.9217 (m) REVERT: B 475 ASN cc_start: 0.8997 (m-40) cc_final: 0.8658 (m110) REVERT: B 493 MET cc_start: 0.9184 (tmm) cc_final: 0.8512 (tmm) REVERT: B 570 MET cc_start: 0.8921 (mmm) cc_final: 0.8418 (tpt) REVERT: B 576 LEU cc_start: 0.9603 (mt) cc_final: 0.9348 (mt) REVERT: B 623 TRP cc_start: 0.9013 (t-100) cc_final: 0.8796 (t-100) REVERT: B 656 LEU cc_start: 0.9321 (mt) cc_final: 0.9096 (mt) REVERT: C 17 PHE cc_start: 0.8979 (p90) cc_final: 0.8250 (p90) REVERT: C 20 MET cc_start: 0.9394 (ppp) cc_final: 0.9175 (ppp) REVERT: C 21 PHE cc_start: 0.9041 (m-80) cc_final: 0.8473 (m-80) REVERT: C 56 MET cc_start: 0.1144 (ptm) cc_final: 0.0571 (ttp) REVERT: C 74 MET cc_start: 0.9295 (mpp) cc_final: 0.9073 (mpp) REVERT: C 89 VAL cc_start: 0.7161 (m) cc_final: 0.6859 (t) REVERT: C 95 MET cc_start: 0.8651 (ttp) cc_final: 0.7944 (ttp) REVERT: C 154 PHE cc_start: 0.9337 (t80) cc_final: 0.9024 (t80) REVERT: C 157 MET cc_start: 0.9229 (ptp) cc_final: 0.8781 (ptt) REVERT: C 174 TYR cc_start: 0.8910 (t80) cc_final: 0.8297 (t80) REVERT: C 212 ILE cc_start: 0.8963 (mt) cc_final: 0.8703 (tp) REVERT: C 231 LEU cc_start: 0.9201 (mt) cc_final: 0.8899 (pp) REVERT: C 239 GLU cc_start: 0.8907 (pt0) cc_final: 0.8421 (pt0) REVERT: C 274 ASP cc_start: 0.9083 (p0) cc_final: 0.8832 (p0) REVERT: D 137 MET cc_start: 0.8520 (mmp) cc_final: 0.8052 (mtt) REVERT: D 238 ASN cc_start: 0.8483 (m110) cc_final: 0.7986 (m110) REVERT: E 24 PHE cc_start: 0.9084 (m-80) cc_final: 0.8786 (m-80) REVERT: E 25 TRP cc_start: 0.8129 (p-90) cc_final: 0.7465 (p-90) REVERT: E 46 MET cc_start: 0.8288 (tpp) cc_final: 0.7983 (tpp) REVERT: E 60 ASN cc_start: 0.9318 (t0) cc_final: 0.9063 (t0) outliers start: 0 outliers final: 0 residues processed: 653 average time/residue: 0.2781 time to fit residues: 271.3276 Evaluate side-chains 539 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.775 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 170 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 184 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 78 optimal weight: 5.9990 chunk 41 optimal weight: 2.9990 chunk 147 optimal weight: 6.9990 chunk 195 optimal weight: 9.9990 chunk 113 optimal weight: 0.9990 chunk 109 optimal weight: 0.9980 chunk 122 optimal weight: 3.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3216 r_free = 0.3216 target = 0.095722 restraints weight = 43367.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.099199 restraints weight = 22805.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.101494 restraints weight = 14417.910| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3287 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3287 r_free = 0.3287 target_work(ls_wunit_k1) = 0.099 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3287 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.7279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 17041 Z= 0.157 Angle : 0.663 9.638 23026 Z= 0.346 Chirality : 0.045 0.226 2464 Planarity : 0.004 0.051 2931 Dihedral : 9.965 141.914 2325 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 16.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.18), residues: 2012 helix: 0.86 (0.15), residues: 1163 sheet: -0.19 (0.40), residues: 157 loop : -0.06 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 623 HIS 0.008 0.001 HIS C 201 PHE 0.041 0.002 PHE A 234 TYR 0.028 0.002 TYR A 571 ARG 0.010 0.001 ARG A 350 Details of bonding type rmsd hydrogen bonds : bond 0.03832 ( 912) hydrogen bonds : angle 5.07920 ( 2664) SS BOND : bond 0.00535 ( 3) SS BOND : angle 4.43571 ( 6) covalent geometry : bond 0.00354 (17038) covalent geometry : angle 0.65905 (23020) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 652 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 652 time to evaluate : 1.952 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 8 LYS cc_start: 0.9068 (tptp) cc_final: 0.8597 (tppt) REVERT: A 12 LEU cc_start: 0.9572 (mt) cc_final: 0.9297 (mt) REVERT: A 119 GLU cc_start: 0.8578 (mp0) cc_final: 0.8373 (mm-30) REVERT: A 150 GLN cc_start: 0.8633 (tp40) cc_final: 0.8260 (tp40) REVERT: A 162 LYS cc_start: 0.9317 (tmtt) cc_final: 0.9049 (ttpt) REVERT: A 187 ASP cc_start: 0.8578 (t70) cc_final: 0.8369 (t0) REVERT: A 209 LYS cc_start: 0.9384 (tttm) cc_final: 0.9149 (tttm) REVERT: A 223 VAL cc_start: 0.9280 (p) cc_final: 0.8954 (p) REVERT: A 228 LYS cc_start: 0.9129 (tptt) cc_final: 0.8801 (mmtt) REVERT: A 250 TYR cc_start: 0.8360 (m-80) cc_final: 0.7973 (m-80) REVERT: A 257 ASP cc_start: 0.8909 (m-30) cc_final: 0.7902 (m-30) REVERT: A 290 GLU cc_start: 0.8996 (tm-30) cc_final: 0.8544 (tm-30) REVERT: A 291 LEU cc_start: 0.9494 (mm) cc_final: 0.8970 (mm) REVERT: A 316 GLU cc_start: 0.7811 (pm20) cc_final: 0.7358 (pm20) REVERT: A 322 MET cc_start: 0.8270 (mmm) cc_final: 0.7974 (mmm) REVERT: A 346 LEU cc_start: 0.9439 (mt) cc_final: 0.9235 (mt) REVERT: A 367 VAL cc_start: 0.9527 (m) cc_final: 0.9310 (p) REVERT: A 390 GLN cc_start: 0.8787 (mt0) cc_final: 0.8568 (mt0) REVERT: A 466 MET cc_start: 0.8368 (ppp) cc_final: 0.8039 (ppp) REVERT: A 474 GLN cc_start: 0.8782 (tm-30) cc_final: 0.8320 (tm-30) REVERT: A 479 TYR cc_start: 0.8766 (t80) cc_final: 0.8269 (t80) REVERT: A 498 TYR cc_start: 0.8767 (m-80) cc_final: 0.8535 (m-80) REVERT: A 501 GLN cc_start: 0.9023 (tt0) cc_final: 0.8549 (tt0) REVERT: A 515 ASP cc_start: 0.8822 (m-30) cc_final: 0.8397 (m-30) REVERT: A 645 GLN cc_start: 0.8820 (tp40) cc_final: 0.8267 (tp40) REVERT: A 647 HIS cc_start: 0.8505 (m-70) cc_final: 0.8170 (m90) REVERT: A 669 ARG cc_start: 0.9032 (mmm160) cc_final: 0.8502 (mmt180) REVERT: B 9 TRP cc_start: 0.9484 (p90) cc_final: 0.8911 (p90) REVERT: B 18 ILE cc_start: 0.9519 (mm) cc_final: 0.9278 (mm) REVERT: B 30 LYS cc_start: 0.9203 (tmtt) cc_final: 0.8996 (tptt) REVERT: B 66 GLU cc_start: 0.8311 (tp30) cc_final: 0.7898 (tp30) REVERT: B 87 LYS cc_start: 0.9078 (tppt) cc_final: 0.8589 (tptp) REVERT: B 120 ASP cc_start: 0.8982 (m-30) cc_final: 0.8717 (m-30) REVERT: B 129 PHE cc_start: 0.9106 (m-10) cc_final: 0.8820 (m-80) REVERT: B 147 GLN cc_start: 0.9131 (mt0) cc_final: 0.8609 (mt0) REVERT: B 184 ARG cc_start: 0.9459 (tpp80) cc_final: 0.9101 (tpp80) REVERT: B 186 ILE cc_start: 0.9551 (mt) cc_final: 0.9305 (mt) REVERT: B 190 MET cc_start: 0.9302 (mtm) cc_final: 0.8921 (mtm) REVERT: B 276 LYS cc_start: 0.9421 (ttpt) cc_final: 0.9094 (ttpt) REVERT: B 286 ASP cc_start: 0.8370 (m-30) cc_final: 0.7780 (m-30) REVERT: B 335 GLU cc_start: 0.7912 (tm-30) cc_final: 0.7666 (tm-30) REVERT: B 348 MET cc_start: 0.8993 (ppp) cc_final: 0.8411 (ppp) REVERT: B 349 LEU cc_start: 0.9292 (mt) cc_final: 0.8578 (mt) REVERT: B 370 ASN cc_start: 0.9578 (m-40) cc_final: 0.9212 (m110) REVERT: B 378 PHE cc_start: 0.8917 (p90) cc_final: 0.8602 (p90) REVERT: B 402 GLU cc_start: 0.8312 (mp0) cc_final: 0.7681 (mp0) REVERT: B 426 GLU cc_start: 0.8862 (tp30) cc_final: 0.8630 (tp30) REVERT: B 427 LYS cc_start: 0.9190 (ptpp) cc_final: 0.8859 (ptpp) REVERT: B 437 THR cc_start: 0.9550 (m) cc_final: 0.9188 (m) REVERT: B 468 LEU cc_start: 0.9247 (tp) cc_final: 0.8796 (tp) REVERT: B 475 ASN cc_start: 0.9262 (m-40) cc_final: 0.8950 (m110) REVERT: B 493 MET cc_start: 0.9193 (tmm) cc_final: 0.8516 (tmm) REVERT: B 623 TRP cc_start: 0.8964 (t-100) cc_final: 0.8712 (t-100) REVERT: B 644 ILE cc_start: 0.9462 (mt) cc_final: 0.9237 (mt) REVERT: B 656 LEU cc_start: 0.9359 (mt) cc_final: 0.9148 (mt) REVERT: C 17 PHE cc_start: 0.9022 (p90) cc_final: 0.8303 (p90) REVERT: C 20 MET cc_start: 0.9423 (ppp) cc_final: 0.9221 (ppp) REVERT: C 21 PHE cc_start: 0.9069 (m-80) cc_final: 0.8523 (m-80) REVERT: C 56 MET cc_start: 0.1053 (ptm) cc_final: 0.0537 (ttp) REVERT: C 68 GLU cc_start: 0.9019 (mp0) cc_final: 0.8601 (pm20) REVERT: C 74 MET cc_start: 0.9336 (mpp) cc_final: 0.9094 (mpp) REVERT: C 89 VAL cc_start: 0.7250 (m) cc_final: 0.7001 (t) REVERT: C 95 MET cc_start: 0.8547 (ttp) cc_final: 0.7977 (ttp) REVERT: C 174 TYR cc_start: 0.9004 (t80) cc_final: 0.8426 (t80) REVERT: C 212 ILE cc_start: 0.8965 (mt) cc_final: 0.8758 (tp) REVERT: C 231 LEU cc_start: 0.9204 (mt) cc_final: 0.8879 (pp) REVERT: C 274 ASP cc_start: 0.9122 (p0) cc_final: 0.8886 (p0) REVERT: D 25 ASN cc_start: 0.9316 (m-40) cc_final: 0.8954 (m-40) REVERT: D 96 MET cc_start: 0.8223 (tpt) cc_final: 0.7861 (tpt) REVERT: D 128 ASN cc_start: 0.8556 (t0) cc_final: 0.8237 (t0) REVERT: D 137 MET cc_start: 0.8527 (mmp) cc_final: 0.8133 (mtt) REVERT: E 24 PHE cc_start: 0.9076 (m-80) cc_final: 0.8828 (m-80) REVERT: E 25 TRP cc_start: 0.8075 (p-90) cc_final: 0.7414 (p-90) REVERT: E 46 MET cc_start: 0.8179 (tpp) cc_final: 0.7880 (tpp) REVERT: E 60 ASN cc_start: 0.9310 (t0) cc_final: 0.9059 (t0) outliers start: 0 outliers final: 0 residues processed: 652 average time/residue: 0.2816 time to fit residues: 274.8982 Evaluate side-chains 539 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 539 time to evaluate : 1.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 140 optimal weight: 6.9990 chunk 23 optimal weight: 0.8980 chunk 173 optimal weight: 0.8980 chunk 64 optimal weight: 0.8980 chunk 105 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 198 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 158 ASN A 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 365 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 91 ASN ** D 28 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.135566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.097393 restraints weight = 43060.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101179 restraints weight = 22151.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.103604 restraints weight = 13605.869| |-----------------------------------------------------------------------------| r_work (final): 0.3311 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3308 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3308 r_free = 0.3308 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3308 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.7460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 17041 Z= 0.143 Angle : 0.671 9.420 23026 Z= 0.348 Chirality : 0.045 0.217 2464 Planarity : 0.004 0.052 2931 Dihedral : 9.736 141.038 2325 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.18), residues: 2012 helix: 0.78 (0.15), residues: 1165 sheet: -0.15 (0.46), residues: 127 loop : -0.18 (0.23), residues: 720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 623 HIS 0.009 0.001 HIS C 201 PHE 0.037 0.002 PHE A 234 TYR 0.028 0.001 TYR A 571 ARG 0.008 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03901 ( 912) hydrogen bonds : angle 5.08088 ( 2664) SS BOND : bond 0.00575 ( 3) SS BOND : angle 4.41786 ( 6) covalent geometry : bond 0.00323 (17038) covalent geometry : angle 0.66727 (23020) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4024 Ramachandran restraints generated. 2012 Oldfield, 0 Emsley, 2012 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 646 time to evaluate : 1.811 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: 0.9111 (tptp) cc_final: 0.8650 (tppt) REVERT: A 12 LEU cc_start: 0.9584 (mt) cc_final: 0.9321 (mt) REVERT: A 119 GLU cc_start: 0.8550 (mp0) cc_final: 0.8308 (mm-30) REVERT: A 150 GLN cc_start: 0.8579 (tp40) cc_final: 0.8238 (tp40) REVERT: A 157 LEU cc_start: 0.9270 (tp) cc_final: 0.8913 (tp) REVERT: A 161 ARG cc_start: 0.8307 (ptp-110) cc_final: 0.8046 (ptp-110) REVERT: A 162 LYS cc_start: 0.9269 (tmtt) cc_final: 0.8958 (ttpt) REVERT: A 184 ARG cc_start: 0.9299 (mmm-85) cc_final: 0.8868 (mmm160) REVERT: A 187 ASP cc_start: 0.8694 (t70) cc_final: 0.8404 (t0) REVERT: A 223 VAL cc_start: 0.9249 (p) cc_final: 0.8962 (p) REVERT: A 228 LYS cc_start: 0.9168 (tptt) cc_final: 0.8838 (mmtt) REVERT: A 250 TYR cc_start: 0.8418 (m-80) cc_final: 0.8008 (m-80) REVERT: A 290 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8472 (tm-30) REVERT: A 291 LEU cc_start: 0.9471 (mm) cc_final: 0.8943 (mm) REVERT: A 301 PHE cc_start: 0.8670 (m-80) cc_final: 0.8312 (m-80) REVERT: A 390 GLN cc_start: 0.8802 (mt0) cc_final: 0.8570 (mt0) REVERT: A 456 LYS cc_start: 0.9140 (ptpp) cc_final: 0.8772 (ptpp) REVERT: A 466 MET cc_start: 0.8422 (ppp) cc_final: 0.8153 (ppp) REVERT: A 474 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8280 (tm-30) REVERT: A 479 TYR cc_start: 0.8866 (t80) cc_final: 0.8579 (t80) REVERT: A 498 TYR cc_start: 0.8739 (m-80) cc_final: 0.8473 (m-80) REVERT: A 501 GLN cc_start: 0.9030 (tt0) cc_final: 0.8418 (tm-30) REVERT: A 515 ASP cc_start: 0.8760 (m-30) cc_final: 0.8308 (m-30) REVERT: A 526 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8234 (tm-30) REVERT: A 645 GLN cc_start: 0.8813 (tp40) cc_final: 0.8464 (tp-100) REVERT: A 647 HIS cc_start: 0.8386 (m-70) cc_final: 0.8162 (m90) REVERT: A 661 THR cc_start: 0.9594 (p) cc_final: 0.9107 (p) REVERT: A 662 MET cc_start: 0.8011 (ptp) cc_final: 0.7802 (pmm) REVERT: A 669 ARG cc_start: 0.9045 (mmm160) cc_final: 0.8531 (mmt180) REVERT: B 9 TRP cc_start: 0.9479 (p90) cc_final: 0.8886 (p90) REVERT: B 18 ILE cc_start: 0.9535 (mm) cc_final: 0.9049 (tp) REVERT: B 40 TYR cc_start: 0.9237 (t80) cc_final: 0.9034 (t80) REVERT: B 66 GLU cc_start: 0.8385 (tp30) cc_final: 0.7917 (tp30) REVERT: B 87 LYS cc_start: 0.9058 (tppt) cc_final: 0.8560 (tptp) REVERT: B 117 ARG cc_start: 0.8111 (mmm160) cc_final: 0.7692 (mmm-85) REVERT: B 120 ASP cc_start: 0.8972 (m-30) cc_final: 0.8549 (m-30) REVERT: B 129 PHE cc_start: 0.9104 (m-10) cc_final: 0.8805 (m-80) REVERT: B 147 GLN cc_start: 0.9089 (mt0) cc_final: 0.8386 (mt0) REVERT: B 186 ILE cc_start: 0.9527 (mt) cc_final: 0.9285 (mt) REVERT: B 190 MET cc_start: 0.9252 (mtm) cc_final: 0.8935 (mtm) REVERT: B 227 MET cc_start: 0.9154 (mtp) cc_final: 0.8954 (mtp) REVERT: B 276 LYS cc_start: 0.9384 (ttpt) cc_final: 0.9063 (ttpt) REVERT: B 286 ASP cc_start: 0.8329 (m-30) cc_final: 0.7740 (m-30) REVERT: B 335 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7619 (tm-30) REVERT: B 348 MET cc_start: 0.8994 (ppp) cc_final: 0.8388 (ppp) REVERT: B 349 LEU cc_start: 0.9274 (mt) cc_final: 0.8554 (mt) REVERT: B 370 ASN cc_start: 0.9557 (m-40) cc_final: 0.9171 (m110) REVERT: B 375 LYS cc_start: 0.9032 (mmmm) cc_final: 0.8366 (mmmm) REVERT: B 378 PHE cc_start: 0.8895 (p90) cc_final: 0.8392 (p90) REVERT: B 402 GLU cc_start: 0.8364 (mp0) cc_final: 0.7751 (mp0) REVERT: B 426 GLU cc_start: 0.8871 (tp30) cc_final: 0.8670 (tp30) REVERT: B 427 LYS cc_start: 0.9156 (ptpp) cc_final: 0.8863 (ptpp) REVERT: B 437 THR cc_start: 0.9476 (m) cc_final: 0.9139 (m) REVERT: B 452 ARG cc_start: 0.8526 (ttt90) cc_final: 0.7991 (ttt90) REVERT: B 468 LEU cc_start: 0.9166 (tp) cc_final: 0.8725 (tp) REVERT: B 475 ASN cc_start: 0.9199 (m-40) cc_final: 0.8888 (m110) REVERT: B 489 ASN cc_start: 0.9115 (t0) cc_final: 0.8821 (t0) REVERT: B 493 MET cc_start: 0.9185 (tmm) cc_final: 0.8455 (tmm) REVERT: B 623 TRP cc_start: 0.8910 (t-100) cc_final: 0.8311 (t-100) REVERT: B 656 LEU cc_start: 0.9350 (mt) cc_final: 0.9084 (mt) REVERT: C 17 PHE cc_start: 0.9040 (p90) cc_final: 0.8314 (p90) REVERT: C 20 MET cc_start: 0.9434 (ppp) cc_final: 0.9234 (ppp) REVERT: C 21 PHE cc_start: 0.9076 (m-80) cc_final: 0.8526 (m-80) REVERT: C 46 TYR cc_start: 0.8162 (m-80) cc_final: 0.7939 (m-80) REVERT: C 56 MET cc_start: 0.1023 (ptm) cc_final: 0.0478 (ttp) REVERT: C 68 GLU cc_start: 0.8989 (mp0) cc_final: 0.8786 (mp0) REVERT: C 74 MET cc_start: 0.9337 (mpp) cc_final: 0.9057 (mpp) REVERT: C 89 VAL cc_start: 0.7085 (m) cc_final: 0.6798 (t) REVERT: C 157 MET cc_start: 0.9217 (ptp) cc_final: 0.8747 (ptt) REVERT: C 174 TYR cc_start: 0.9004 (t80) cc_final: 0.8414 (t80) REVERT: C 231 LEU cc_start: 0.9172 (mt) cc_final: 0.8875 (pp) REVERT: C 239 GLU cc_start: 0.8850 (pt0) cc_final: 0.8348 (pt0) REVERT: C 274 ASP cc_start: 0.9125 (p0) cc_final: 0.8871 (p0) REVERT: D 25 ASN cc_start: 0.9274 (m-40) cc_final: 0.8849 (m-40) REVERT: D 96 MET cc_start: 0.7973 (tpt) cc_final: 0.7418 (tpt) REVERT: D 137 MET cc_start: 0.8540 (mmp) cc_final: 0.8158 (mtt) REVERT: D 238 ASN cc_start: 0.8510 (m110) cc_final: 0.8046 (m110) REVERT: E 24 PHE cc_start: 0.9035 (m-80) cc_final: 0.8818 (m-80) REVERT: E 25 TRP cc_start: 0.8126 (p-90) cc_final: 0.7466 (p-90) REVERT: E 46 MET cc_start: 0.8151 (tpp) cc_final: 0.7878 (tpp) REVERT: E 60 ASN cc_start: 0.9312 (t0) cc_final: 0.9064 (t0) outliers start: 0 outliers final: 0 residues processed: 646 average time/residue: 0.2792 time to fit residues: 270.5368 Evaluate side-chains 548 residues out of total 1789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 548 time to evaluate : 1.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 200 random chunks: chunk 85 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 198 optimal weight: 8.9990 chunk 146 optimal weight: 0.4980 chunk 165 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 148 optimal weight: 10.0000 chunk 124 optimal weight: 0.9990 chunk 144 optimal weight: 20.0000 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 158 ASN A 180 ASN ** A 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 338 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 588 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 109 ASN B 150 GLN ** B 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 387 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 28 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.133984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.096587 restraints weight = 43000.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.100268 restraints weight = 21926.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.102620 restraints weight = 13602.190| |-----------------------------------------------------------------------------| r_work (final): 0.3284 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3282 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3282 r_free = 0.3282 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 = 0.3282 r_free = 0.3282 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3282 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.7568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 17041 Z= 0.171 Angle : 0.685 9.881 23026 Z= 0.357 Chirality : 0.045 0.243 2464 Planarity : 0.004 0.053 2931 Dihedral : 9.796 142.526 2325 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 16.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.66 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.18), residues: 2012 helix: 0.74 (0.15), residues: 1173 sheet: -0.13 (0.47), residues: 127 loop : -0.20 (0.23), residues: 712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 623 HIS 0.008 0.001 HIS C 201 PHE 0.036 0.002 PHE A 234 TYR 0.024 0.002 TYR D 105 ARG 0.007 0.001 ARG C 261 Details of bonding type rmsd hydrogen bonds : bond 0.03918 ( 912) hydrogen bonds : angle 5.11822 ( 2664) SS BOND : bond 0.00600 ( 3) SS BOND : angle 4.27490 ( 6) covalent geometry : bond 0.00384 (17038) covalent geometry : angle 0.68154 (23020) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7324.73 seconds wall clock time: 128 minutes 44.23 seconds (7724.23 seconds total)