Starting phenix.real_space_refine on Sat May 17 10:50:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ene_28271/05_2025/8ene_28271.cif" } resolution = 2.64 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= 0.043 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 76 5.16 5 C 9805 2.51 5 N 2599 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 15404 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "B" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "C" Number of atoms: 3804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3804 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "D" Number of atoms: 3808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 493, 3808 Classifications: {'peptide': 493} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 23, 'TRANS': 469} Chain: "A" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 44 Unusual residues: {'NAD': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.50, per 1000 atoms: 0.62 Number of scatterers: 15404 At special positions: 0 Unit cell: (109.08, 106.92, 100.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 76 16.00 P 8 15.00 O 2916 8.00 N 2599 7.00 C 9805 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.82 Conformation dependent library (CDL) restraints added in 2.0 seconds 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3568 Finding SS restraints... Secondary structure from input PDB file: 72 helices and 22 sheets defined 45.2% alpha, 16.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 56 through 71 Processing helix chain 'A' and resid 75 through 80 Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 99 through 112 Processing helix chain 'A' and resid 114 through 121 Processing helix chain 'A' and resid 121 through 137 Processing helix chain 'A' and resid 171 through 186 Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 199 through 213 removed outlier: 3.512A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLY A 213 " --> pdb=" O ILE A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 228 through 236 Processing helix chain 'A' and resid 247 through 261 Processing helix chain 'A' and resid 283 through 297 Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 315 through 330 Processing helix chain 'A' and resid 347 through 365 Processing helix chain 'A' and resid 394 through 398 Processing helix chain 'A' and resid 413 through 423 Processing helix chain 'A' and resid 436 through 447 Processing helix chain 'A' and resid 479 through 485 removed outlier: 3.697A pdb=" N GLU A 485 " --> pdb=" O TYR A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 71 Processing helix chain 'B' and resid 75 through 80 Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 99 through 112 Processing helix chain 'B' and resid 114 through 121 Processing helix chain 'B' and resid 121 through 137 Processing helix chain 'B' and resid 171 through 186 Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 199 through 213 removed outlier: 3.545A pdb=" N GLY B 213 " --> pdb=" O ILE B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 228 through 236 Processing helix chain 'B' and resid 247 through 261 Processing helix chain 'B' and resid 283 through 297 Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 315 through 330 Processing helix chain 'B' and resid 347 through 365 Processing helix chain 'B' and resid 394 through 398 Processing helix chain 'B' and resid 413 through 423 Processing helix chain 'B' and resid 436 through 447 Processing helix chain 'B' and resid 479 through 485 removed outlier: 3.713A pdb=" N GLU B 485 " --> pdb=" O TYR B 481 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 71 Processing helix chain 'C' and resid 75 through 80 Processing helix chain 'C' and resid 81 through 99 Processing helix chain 'C' and resid 99 through 112 Processing helix chain 'C' and resid 114 through 121 Processing helix chain 'C' and resid 121 through 137 Processing helix chain 'C' and resid 171 through 186 Proline residue: C 182 - end of helix Processing helix chain 'C' and resid 199 through 213 removed outlier: 3.551A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLY C 213 " --> pdb=" O ILE C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 228 through 236 Processing helix chain 'C' and resid 247 through 260 Processing helix chain 'C' and resid 283 through 297 Processing helix chain 'C' and resid 298 through 301 Processing helix chain 'C' and resid 315 through 330 Processing helix chain 'C' and resid 347 through 364 Processing helix chain 'C' and resid 394 through 398 Processing helix chain 'C' and resid 413 through 422 Processing helix chain 'C' and resid 437 through 447 Processing helix chain 'C' and resid 479 through 485 removed outlier: 3.670A pdb=" N GLU C 485 " --> pdb=" O TYR C 481 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 71 Processing helix chain 'D' and resid 75 through 80 Processing helix chain 'D' and resid 81 through 99 Processing helix chain 'D' and resid 99 through 112 Processing helix chain 'D' and resid 114 through 121 Processing helix chain 'D' and resid 121 through 137 Processing helix chain 'D' and resid 171 through 186 Proline residue: D 182 - end of helix Processing helix chain 'D' and resid 199 through 213 removed outlier: 3.535A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY D 213 " --> pdb=" O ILE D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 228 through 236 Processing helix chain 'D' and resid 247 through 261 Processing helix chain 'D' and resid 283 through 297 Processing helix chain 'D' and resid 298 through 301 Processing helix chain 'D' and resid 315 through 330 Processing helix chain 'D' and resid 347 through 365 Processing helix chain 'D' and resid 394 through 398 Processing helix chain 'D' and resid 413 through 423 Processing helix chain 'D' and resid 437 through 447 Processing helix chain 'D' and resid 479 through 485 removed outlier: 3.683A pdb=" N GLU D 485 " --> pdb=" O TYR D 481 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 25 Processing sheet with id=AA2, first strand: chain 'A' and resid 37 through 42 removed outlier: 6.124A pdb=" N PHE A 38 " --> pdb=" O GLN A 51 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLN A 51 " --> pdb=" O PHE A 38 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N VAL A 40 " --> pdb=" O LEU A 49 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU A 47 " --> pdb=" O ASN A 42 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 145 removed outlier: 4.238A pdb=" N THR A 153 " --> pdb=" O ILE A 145 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL B 452 " --> pdb=" O VAL A 489 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR A 491 " --> pdb=" O VAL B 452 " (cutoff:3.500A) removed outlier: 7.727A pdb=" N VAL B 454 " --> pdb=" O THR A 491 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR A 493 " --> pdb=" O VAL B 454 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER B 274 " --> pdb=" O ALA B 306 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N SER B 307 " --> pdb=" O VAL B 405 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN B 407 " --> pdb=" O SER B 307 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL B 386 " --> pdb=" O GLU B 369 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 219 through 221 removed outlier: 6.281A pdb=" N CYS A 163 " --> pdb=" O VAL A 191 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N LYS A 193 " --> pdb=" O CYS A 163 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N GLN A 165 " --> pdb=" O LYS A 193 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N LEU A 268 " --> pdb=" O ASN A 474 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 367 through 370 removed outlier: 6.467A pdb=" N VAL A 386 " --> pdb=" O GLU A 369 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N SER A 307 " --> pdb=" O GLN A 407 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N MET A 409 " --> pdb=" O SER A 307 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N ILE A 309 " --> pdb=" O MET A 409 " (cutoff:3.500A) removed outlier: 7.226A pdb=" N PHE A 411 " --> pdb=" O ILE A 309 " (cutoff:3.500A) removed outlier: 6.223A pdb=" N VAL A 311 " --> pdb=" O PHE A 411 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N SER A 274 " --> pdb=" O ALA A 306 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N THR B 153 " --> pdb=" O ILE B 145 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 374 through 375 removed outlier: 4.043A pdb=" N PHE A 381 " --> pdb=" O TRP A 375 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 23 through 25 Processing sheet with id=AA8, first strand: chain 'B' and resid 37 through 42 removed outlier: 6.212A pdb=" N PHE B 38 " --> pdb=" O GLN B 51 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN B 51 " --> pdb=" O PHE B 38 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 40 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLU B 47 " --> pdb=" O ASN B 42 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 219 through 221 removed outlier: 6.329A pdb=" N CYS B 163 " --> pdb=" O VAL B 191 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N LYS B 193 " --> pdb=" O CYS B 163 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N GLN B 165 " --> pdb=" O LYS B 193 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 374 through 375 removed outlier: 4.064A pdb=" N PHE B 381 " --> pdb=" O TRP B 375 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 426 through 427 removed outlier: 3.735A pdb=" N GLY B 427 " --> pdb=" O PHE B 469 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 466 through 467 Processing sheet with id=AB4, first strand: chain 'C' and resid 23 through 25 Processing sheet with id=AB5, first strand: chain 'C' and resid 37 through 42 removed outlier: 6.346A pdb=" N PHE C 38 " --> pdb=" O GLN C 51 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLN C 51 " --> pdb=" O PHE C 38 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL C 40 " --> pdb=" O LEU C 49 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU C 47 " --> pdb=" O ASN C 42 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 143 through 145 removed outlier: 4.261A pdb=" N THR C 153 " --> pdb=" O ILE C 145 " (cutoff:3.500A) removed outlier: 8.154A pdb=" N VAL D 452 " --> pdb=" O VAL C 489 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N THR C 491 " --> pdb=" O VAL D 452 " (cutoff:3.500A) removed outlier: 7.740A pdb=" N VAL D 454 " --> pdb=" O THR C 491 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N THR C 493 " --> pdb=" O VAL D 454 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER D 274 " --> pdb=" O ALA D 306 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N SER D 307 " --> pdb=" O VAL D 405 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N GLN D 407 " --> pdb=" O SER D 307 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N VAL D 386 " --> pdb=" O GLU D 369 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 219 through 221 removed outlier: 6.309A pdb=" N CYS C 163 " --> pdb=" O VAL C 191 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N LYS C 193 " --> pdb=" O CYS C 163 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN C 165 " --> pdb=" O LYS C 193 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 367 through 370 removed outlier: 6.468A pdb=" N VAL C 386 " --> pdb=" O GLU C 369 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N SER C 307 " --> pdb=" O GLN C 407 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N MET C 409 " --> pdb=" O SER C 307 " (cutoff:3.500A) removed outlier: 6.015A pdb=" N ILE C 309 " --> pdb=" O MET C 409 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N PHE C 411 " --> pdb=" O ILE C 309 " (cutoff:3.500A) removed outlier: 6.205A pdb=" N VAL C 311 " --> pdb=" O PHE C 411 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N SER C 274 " --> pdb=" O ALA C 306 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N THR D 153 " --> pdb=" O ILE D 145 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 374 through 375 removed outlier: 4.000A pdb=" N PHE C 381 " --> pdb=" O TRP C 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 23 through 25 Processing sheet with id=AC2, first strand: chain 'D' and resid 37 through 42 removed outlier: 6.143A pdb=" N PHE D 38 " --> pdb=" O GLN D 51 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N GLN D 51 " --> pdb=" O PHE D 38 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL D 40 " --> pdb=" O LEU D 49 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N GLU D 47 " --> pdb=" O ASN D 42 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 219 through 221 removed outlier: 6.347A pdb=" N CYS D 163 " --> pdb=" O VAL D 191 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N LYS D 193 " --> pdb=" O CYS D 163 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLN D 165 " --> pdb=" O LYS D 193 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU D 268 " --> pdb=" O ASN D 474 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 374 through 375 removed outlier: 3.995A pdb=" N PHE D 381 " --> pdb=" O TRP D 375 " (cutoff:3.500A) 797 hydrogen bonds defined for protein. 2283 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: 5.14 Time building geometry restraints manager: 4.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5004 1.34 - 1.46: 3410 1.46 - 1.58: 7214 1.58 - 1.69: 12 1.69 - 1.81: 108 Bond restraints: 15748 Sorted by residual: bond pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3N NAD A 601 " pdb=" C4N NAD A 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C3N NAD D 601 " pdb=" C4N NAD D 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C3N NAD B 601 " pdb=" C4N NAD B 601 " ideal model delta sigma weight residual 1.390 1.498 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4N NAD B 601 " pdb=" C5N NAD B 601 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 15743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21058 2.06 - 4.11: 254 4.11 - 6.17: 24 6.17 - 8.23: 8 8.23 - 10.28: 8 Bond angle restraints: 21352 Sorted by residual: angle pdb=" PA NAD A 601 " pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " ideal model delta sigma weight residual 126.50 136.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD D 601 " pdb=" O3 NAD D 601 " pdb=" PN NAD D 601 " ideal model delta sigma weight residual 126.50 136.74 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD B 601 " pdb=" O3 NAD B 601 " pdb=" PN NAD B 601 " ideal model delta sigma weight residual 126.50 136.70 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" PA NAD C 601 " pdb=" O3 NAD C 601 " pdb=" PN NAD C 601 " ideal model delta sigma weight residual 126.50 136.68 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " pdb=" C5N NAD C 601 " ideal model delta sigma weight residual 119.68 110.28 9.40 3.00e+00 1.11e-01 9.81e+00 ... (remaining 21347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 8304 11.87 - 23.74: 792 23.74 - 35.61: 231 35.61 - 47.48: 98 47.48 - 59.35: 83 Dihedral angle restraints: 9508 sinusoidal: 3908 harmonic: 5600 Sorted by residual: dihedral pdb=" CA THR D 144 " pdb=" C THR D 144 " pdb=" N ILE D 145 " pdb=" CA ILE D 145 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 144 " pdb=" C THR C 144 " pdb=" N ILE C 145 " pdb=" CA ILE C 145 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR A 144 " pdb=" C THR A 144 " pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1504 0.031 - 0.061: 550 0.061 - 0.092: 159 0.092 - 0.123: 144 0.123 - 0.154: 7 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C2B NAD D 601 " pdb=" C1B NAD D 601 " pdb=" C3B NAD D 601 " pdb=" O2B NAD D 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" C2B NAD B 601 " pdb=" C1B NAD B 601 " pdb=" C3B NAD B 601 " pdb=" O2B NAD B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" C2B NAD C 601 " pdb=" C1B NAD C 601 " pdb=" C3B NAD C 601 " pdb=" O2B NAD C 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2361 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " -0.025 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" C2N NAD B 601 " -0.057 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.059 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " -0.068 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " -0.010 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " 0.109 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.100 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 601 " 0.024 2.00e-02 2.50e+03 5.70e-02 6.49e+01 pdb=" C2N NAD D 601 " 0.047 2.00e-02 2.50e+03 pdb=" C3N NAD D 601 " 0.054 2.00e-02 2.50e+03 pdb=" C4N NAD D 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD D 601 " 0.020 2.00e-02 2.50e+03 pdb=" C6N NAD D 601 " -0.101 2.00e-02 2.50e+03 pdb=" C7N NAD D 601 " -0.084 2.00e-02 2.50e+03 pdb=" N1N NAD D 601 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 601 " -0.009 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" C2N NAD A 601 " 0.056 2.00e-02 2.50e+03 pdb=" C3N NAD A 601 " 0.057 2.00e-02 2.50e+03 pdb=" C4N NAD A 601 " 0.034 2.00e-02 2.50e+03 pdb=" C5N NAD A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6N NAD A 601 " -0.049 2.00e-02 2.50e+03 pdb=" C7N NAD A 601 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NAD A 601 " -0.000 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3481 2.79 - 3.32: 14534 3.32 - 3.84: 26298 3.84 - 4.37: 32370 4.37 - 4.90: 54688 Nonbonded interactions: 131371 Sorted by model distance: nonbonded pdb=" O SER B 307 " pdb=" NE2 GLN B 407 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP C 281 " pdb=" OG1 THR C 434 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 281 " pdb=" OG1 THR A 434 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 461 " pdb=" OE1 GLN B 463 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 307 " pdb=" NE2 GLN A 407 " model vdw 2.290 3.120 ... (remaining 131366 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 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = (chain 'B' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) selection = chain 'C' selection = (chain 'D' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 501 or resid 601)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.910 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.160 Process input model: 35.950 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 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 : 0.005 0.109 15748 Z= 0.228 Angle : 0.598 10.283 21352 Z= 0.308 Chirality : 0.041 0.154 2364 Planarity : 0.005 0.065 2736 Dihedral : 12.542 59.347 5940 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 6.01 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.46 (0.20), residues: 1964 helix: 1.11 (0.19), residues: 828 sheet: 0.10 (0.26), residues: 420 loop : -0.39 (0.24), residues: 716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 453 HIS 0.002 0.001 HIS D 204 PHE 0.009 0.001 PHE D 290 TYR 0.016 0.001 TYR D 351 ARG 0.004 0.000 ARG D 131 Details of bonding type rmsd hydrogen bonds : bond 0.14039 ( 797) hydrogen bonds : angle 6.65277 ( 2283) covalent geometry : bond 0.00463 (15748) covalent geometry : angle 0.59751 (21352) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 381 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 346 time to evaluate : 1.917 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4634 (pp) REVERT: A 409 MET cc_start: 0.7342 (mtp) cc_final: 0.7068 (mtm) REVERT: A 441 ILE cc_start: 0.7706 (mm) cc_final: 0.7497 (mm) REVERT: B 13 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4532 (pp) REVERT: B 341 THR cc_start: 0.7504 (p) cc_final: 0.7219 (p) REVERT: B 441 ILE cc_start: 0.7592 (mm) cc_final: 0.7357 (mm) REVERT: C 13 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4543 (pp) REVERT: C 330 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.5236 (t80) REVERT: C 409 MET cc_start: 0.7381 (mtp) cc_final: 0.7121 (mtm) REVERT: C 441 ILE cc_start: 0.7596 (mm) cc_final: 0.7348 (mm) REVERT: D 330 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5385 (t80) REVERT: D 409 MET cc_start: 0.7305 (mtp) cc_final: 0.7051 (mtm) outliers start: 35 outliers final: 12 residues processed: 369 average time/residue: 1.2278 time to fit residues: 500.8172 Evaluate side-chains 249 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 232 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 330 TYR Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 330 TYR Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 330 TYR Chi-restraints excluded: chain D residue 370 CYS Chi-restraints excluded: chain D residue 402 PHE Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 165 optimal weight: 1.9990 chunk 148 optimal weight: 4.9990 chunk 82 optimal weight: 0.1980 chunk 50 optimal weight: 3.9990 chunk 100 optimal weight: 2.9990 chunk 79 optimal weight: 4.9990 chunk 153 optimal weight: 0.8980 chunk 59 optimal weight: 0.9980 chunk 93 optimal weight: 3.9990 chunk 114 optimal weight: 0.8980 chunk 177 optimal weight: 4.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 HIS A 299 GLN A 350 GLN A 389 ASN A 474 ASN B 157 HIS B 220 ASN B 299 GLN B 301 GLN B 342 GLN B 389 ASN B 474 ASN C 157 HIS C 299 GLN C 301 GLN C 342 GLN C 350 GLN D 299 GLN D 301 GLN D 342 GLN D 389 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.158351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138401 restraints weight = 17903.121| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.02 r_work: 0.3677 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3574 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 15748 Z= 0.150 Angle : 0.542 6.749 21352 Z= 0.290 Chirality : 0.043 0.160 2364 Planarity : 0.004 0.038 2736 Dihedral : 9.513 57.661 2353 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.23 % Allowed : 14.04 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.20), residues: 1964 helix: 1.29 (0.18), residues: 864 sheet: 0.14 (0.26), residues: 420 loop : -0.42 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 178 HIS 0.008 0.001 HIS C 484 PHE 0.010 0.001 PHE D 290 TYR 0.019 0.002 TYR D 351 ARG 0.003 0.001 ARG C 420 Details of bonding type rmsd hydrogen bonds : bond 0.04480 ( 797) hydrogen bonds : angle 5.00749 ( 2283) covalent geometry : bond 0.00351 (15748) covalent geometry : angle 0.54191 (21352) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 247 time to evaluate : 1.784 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4818 (pp) REVERT: A 19 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.5971 (mm-40) REVERT: A 58 GLU cc_start: 0.7044 (mp0) cc_final: 0.6841 (pm20) REVERT: A 87 ARG cc_start: 0.7968 (tpt90) cc_final: 0.7744 (mmm160) REVERT: A 156 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8273 (mtp85) REVERT: A 262 ASN cc_start: 0.7418 (OUTLIER) cc_final: 0.7130 (p0) REVERT: A 325 GLU cc_start: 0.6895 (tt0) cc_final: 0.6408 (pt0) REVERT: A 399 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8091 (mt-10) REVERT: A 409 MET cc_start: 0.8265 (mtp) cc_final: 0.7628 (mtm) REVERT: A 481 TYR cc_start: 0.7024 (t80) cc_final: 0.6420 (t80) REVERT: A 485 GLU cc_start: 0.7873 (OUTLIER) cc_final: 0.6551 (mp0) REVERT: B 13 LEU cc_start: 0.5155 (OUTLIER) cc_final: 0.4806 (pp) REVERT: B 19 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6121 (mm-40) REVERT: B 262 ASN cc_start: 0.7989 (t0) cc_final: 0.7773 (t0) REVERT: B 325 GLU cc_start: 0.6906 (tt0) cc_final: 0.6412 (pt0) REVERT: B 330 TYR cc_start: 0.7202 (OUTLIER) cc_final: 0.6047 (t80) REVERT: B 341 THR cc_start: 0.7388 (p) cc_final: 0.6740 (p) REVERT: B 363 LYS cc_start: 0.7405 (mtpp) cc_final: 0.6783 (mmtm) REVERT: C 13 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4664 (pp) REVERT: C 19 GLN cc_start: 0.6956 (OUTLIER) cc_final: 0.5629 (mm-40) REVERT: C 58 GLU cc_start: 0.6989 (mp0) cc_final: 0.6783 (pm20) REVERT: C 156 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8294 (mtp85) REVERT: C 262 ASN cc_start: 0.8102 (t0) cc_final: 0.7883 (t0) REVERT: C 322 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7237 (mtt-85) REVERT: C 325 GLU cc_start: 0.6690 (tt0) cc_final: 0.6275 (pt0) REVERT: C 329 LYS cc_start: 0.7567 (mtpt) cc_final: 0.7334 (mtpt) REVERT: C 409 MET cc_start: 0.8229 (mtp) cc_final: 0.7549 (mtm) REVERT: C 484 HIS cc_start: 0.7206 (m170) cc_final: 0.6932 (m170) REVERT: D 19 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6098 (mm-40) REVERT: D 58 GLU cc_start: 0.7017 (mp0) cc_final: 0.6806 (pm20) REVERT: D 87 ARG cc_start: 0.7944 (tpt90) cc_final: 0.7735 (mmm160) REVERT: D 102 LEU cc_start: 0.7594 (OUTLIER) cc_final: 0.7271 (tt) REVERT: D 156 ARG cc_start: 0.8885 (OUTLIER) cc_final: 0.8316 (mtp85) REVERT: D 321 ARG cc_start: 0.7238 (mpt180) cc_final: 0.6930 (mpt90) REVERT: D 329 LYS cc_start: 0.7555 (mtpt) cc_final: 0.7341 (mtpt) REVERT: D 409 MET cc_start: 0.8054 (mtp) cc_final: 0.7436 (mtm) REVERT: D 438 ASP cc_start: 0.6606 (m-30) cc_final: 0.5885 (t0) REVERT: D 441 ILE cc_start: 0.7239 (mm) cc_final: 0.7010 (mm) REVERT: D 481 TYR cc_start: 0.6930 (t80) cc_final: 0.6336 (t80) REVERT: D 485 GLU cc_start: 0.7806 (OUTLIER) cc_final: 0.6495 (mp0) outliers start: 69 outliers final: 31 residues processed: 279 average time/residue: 1.2170 time to fit residues: 375.8155 Evaluate side-chains 282 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 235 time to evaluate : 1.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 315 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 127 optimal weight: 5.9990 chunk 62 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 0.3980 chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 128 optimal weight: 0.5980 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN D 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.160164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.140493 restraints weight = 18013.375| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.99 r_work: 0.3738 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3634 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 15748 Z= 0.140 Angle : 0.511 6.054 21352 Z= 0.274 Chirality : 0.042 0.159 2364 Planarity : 0.004 0.040 2736 Dihedral : 8.404 58.602 2344 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.23 % Allowed : 16.37 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.20), residues: 1964 helix: 1.44 (0.18), residues: 864 sheet: 0.13 (0.26), residues: 420 loop : -0.45 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 178 HIS 0.006 0.001 HIS B 484 PHE 0.011 0.001 PHE D 290 TYR 0.020 0.002 TYR B 351 ARG 0.003 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04110 ( 797) hydrogen bonds : angle 4.80774 ( 2283) covalent geometry : bond 0.00329 (15748) covalent geometry : angle 0.51053 (21352) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 315 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 246 time to evaluate : 1.874 Fit side-chains REVERT: A 19 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5947 (mm-40) REVERT: A 58 GLU cc_start: 0.6987 (mp0) cc_final: 0.6700 (OUTLIER) REVERT: A 156 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8317 (mtp85) REVERT: A 321 ARG cc_start: 0.6791 (mtm-85) cc_final: 0.6135 (mtp-110) REVERT: A 325 GLU cc_start: 0.6811 (tt0) cc_final: 0.6354 (pt0) REVERT: A 399 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 409 MET cc_start: 0.8292 (mtp) cc_final: 0.7672 (mtm) REVERT: B 13 LEU cc_start: 0.5140 (OUTLIER) cc_final: 0.4833 (pp) REVERT: B 19 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6062 (mm-40) REVERT: B 121 ASN cc_start: 0.7778 (m110) cc_final: 0.7378 (m-40) REVERT: B 262 ASN cc_start: 0.7946 (t0) cc_final: 0.7734 (t0) REVERT: B 321 ARG cc_start: 0.6760 (mtm-85) cc_final: 0.6113 (mtp-110) REVERT: B 325 GLU cc_start: 0.6877 (tt0) cc_final: 0.6356 (pt0) REVERT: B 330 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.6093 (t80) REVERT: B 341 THR cc_start: 0.7389 (p) cc_final: 0.6777 (p) REVERT: B 363 LYS cc_start: 0.7391 (mtpp) cc_final: 0.6818 (mmtm) REVERT: C 19 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.5753 (mm-40) REVERT: C 156 ARG cc_start: 0.8852 (OUTLIER) cc_final: 0.8356 (mtp85) REVERT: C 262 ASN cc_start: 0.8173 (t0) cc_final: 0.7941 (t0) REVERT: C 321 ARG cc_start: 0.6776 (mtm-85) cc_final: 0.6196 (mtp-110) REVERT: C 322 ARG cc_start: 0.7504 (ttm170) cc_final: 0.7243 (mtt-85) REVERT: C 325 GLU cc_start: 0.6686 (tt0) cc_final: 0.6242 (pt0) REVERT: C 329 LYS cc_start: 0.7577 (mtpt) cc_final: 0.7310 (mtpt) REVERT: C 399 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 409 MET cc_start: 0.8266 (mtp) cc_final: 0.7615 (mtm) REVERT: C 438 ASP cc_start: 0.6416 (m-30) cc_final: 0.5878 (t0) REVERT: C 484 HIS cc_start: 0.7280 (m170) cc_final: 0.6975 (m170) REVERT: C 485 GLU cc_start: 0.7989 (OUTLIER) cc_final: 0.6745 (mp0) REVERT: D 19 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.6049 (mm-40) REVERT: D 102 LEU cc_start: 0.7728 (OUTLIER) cc_final: 0.7414 (tt) REVERT: D 156 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8308 (mtp85) REVERT: D 329 LYS cc_start: 0.7551 (mtpt) cc_final: 0.7293 (mtpt) REVERT: D 409 MET cc_start: 0.8197 (mtp) cc_final: 0.7604 (mtm) REVERT: D 438 ASP cc_start: 0.6456 (m-30) cc_final: 0.5835 (t0) REVERT: D 441 ILE cc_start: 0.7340 (mm) cc_final: 0.7134 (mm) outliers start: 69 outliers final: 41 residues processed: 284 average time/residue: 1.1663 time to fit residues: 367.9598 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 227 time to evaluate : 1.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 137 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 190 optimal weight: 4.9990 chunk 173 optimal weight: 0.7980 chunk 162 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 chunk 49 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3964 r_free = 0.3964 target = 0.160160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.140689 restraints weight = 17939.482| |-----------------------------------------------------------------------------| r_work (start): 0.3817 rms_B_bonded: 1.96 r_work: 0.3740 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3636 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15748 Z= 0.132 Angle : 0.504 6.394 21352 Z= 0.270 Chirality : 0.042 0.159 2364 Planarity : 0.004 0.040 2736 Dihedral : 7.910 58.732 2342 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.17 % Allowed : 17.17 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.20), residues: 1964 helix: 1.48 (0.18), residues: 864 sheet: 0.09 (0.26), residues: 420 loop : -0.41 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 178 HIS 0.006 0.001 HIS D 484 PHE 0.011 0.001 PHE D 290 TYR 0.021 0.002 TYR B 351 ARG 0.003 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03896 ( 797) hydrogen bonds : angle 4.73248 ( 2283) covalent geometry : bond 0.00308 (15748) covalent geometry : angle 0.50359 (21352) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 232 time to evaluate : 1.827 Fit side-chains REVERT: A 19 GLN cc_start: 0.7062 (OUTLIER) cc_final: 0.5929 (mm-40) REVERT: A 156 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8360 (mtp85) REVERT: A 321 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6133 (mtp-110) REVERT: A 325 GLU cc_start: 0.6808 (tt0) cc_final: 0.6318 (pt0) REVERT: A 399 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: A 409 MET cc_start: 0.8280 (mtp) cc_final: 0.7682 (mtm) REVERT: B 19 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6109 (mm-40) REVERT: B 121 ASN cc_start: 0.7771 (m110) cc_final: 0.7390 (m-40) REVERT: B 262 ASN cc_start: 0.7918 (t0) cc_final: 0.7673 (t0) REVERT: B 321 ARG cc_start: 0.6729 (mtm-85) cc_final: 0.6089 (mtp-110) REVERT: B 325 GLU cc_start: 0.6937 (tt0) cc_final: 0.6474 (pt0) REVERT: B 330 TYR cc_start: 0.7116 (OUTLIER) cc_final: 0.5897 (t80) REVERT: B 341 THR cc_start: 0.7500 (p) cc_final: 0.6770 (p) REVERT: B 363 LYS cc_start: 0.7456 (mtpp) cc_final: 0.6890 (mmtm) REVERT: C 19 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.5752 (mm-40) REVERT: C 58 GLU cc_start: 0.6942 (mp0) cc_final: 0.6715 (pm20) REVERT: C 121 ASN cc_start: 0.7665 (m110) cc_final: 0.7421 (m-40) REVERT: C 156 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8329 (mtp85) REVERT: C 262 ASN cc_start: 0.8236 (t0) cc_final: 0.8014 (t0) REVERT: C 321 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6131 (mtp-110) REVERT: C 325 GLU cc_start: 0.6686 (tt0) cc_final: 0.6226 (pt0) REVERT: C 399 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.8084 (mt-10) REVERT: C 409 MET cc_start: 0.8267 (mtp) cc_final: 0.7648 (mtm) REVERT: C 438 ASP cc_start: 0.6382 (m-30) cc_final: 0.5853 (t0) REVERT: C 484 HIS cc_start: 0.7267 (m170) cc_final: 0.6986 (m170) REVERT: D 19 GLN cc_start: 0.7013 (OUTLIER) cc_final: 0.5911 (mm-40) REVERT: D 58 GLU cc_start: 0.6884 (mp0) cc_final: 0.6663 (pm20) REVERT: D 102 LEU cc_start: 0.7718 (OUTLIER) cc_final: 0.7384 (tt) REVERT: D 156 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8307 (mtp85) REVERT: D 321 ARG cc_start: 0.7108 (mpt180) cc_final: 0.6749 (mpt90) REVERT: D 409 MET cc_start: 0.8186 (mtp) cc_final: 0.7565 (mtm) REVERT: D 438 ASP cc_start: 0.6224 (m-30) cc_final: 0.5763 (t0) REVERT: D 441 ILE cc_start: 0.7314 (mm) cc_final: 0.7106 (mm) REVERT: D 485 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6680 (mp0) outliers start: 68 outliers final: 44 residues processed: 270 average time/residue: 1.2050 time to fit residues: 361.2654 Evaluate side-chains 279 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 223 time to evaluate : 1.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Chi-restraints excluded: chain D residue 488 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 5.9990 chunk 36 optimal weight: 4.9990 chunk 183 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 162 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 64 optimal weight: 10.0000 chunk 76 optimal weight: 0.5980 chunk 185 optimal weight: 3.9990 chunk 135 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.159527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.140047 restraints weight = 18047.853| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 1.97 r_work: 0.3734 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3630 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15748 Z= 0.142 Angle : 0.508 5.739 21352 Z= 0.272 Chirality : 0.042 0.156 2364 Planarity : 0.004 0.038 2736 Dihedral : 7.785 58.243 2342 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.72 % Allowed : 16.92 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.72 (0.20), residues: 1964 helix: 1.51 (0.18), residues: 860 sheet: 0.01 (0.26), residues: 420 loop : -0.43 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 178 HIS 0.007 0.001 HIS D 484 PHE 0.011 0.001 PHE D 411 TYR 0.021 0.002 TYR B 351 ARG 0.003 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 797) hydrogen bonds : angle 4.71461 ( 2283) covalent geometry : bond 0.00339 (15748) covalent geometry : angle 0.50803 (21352) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 230 time to evaluate : 1.615 Fit side-chains REVERT: A 19 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.5889 (mm-40) REVERT: A 156 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8363 (mtp85) REVERT: A 321 ARG cc_start: 0.6761 (mtm-85) cc_final: 0.6116 (mtp-110) REVERT: A 325 GLU cc_start: 0.6819 (tt0) cc_final: 0.6305 (pt0) REVERT: A 349 GLU cc_start: 0.6782 (OUTLIER) cc_final: 0.6289 (mp0) REVERT: A 399 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 409 MET cc_start: 0.8291 (mtp) cc_final: 0.7704 (mtm) REVERT: A 485 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: B 19 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6086 (mm-40) REVERT: B 121 ASN cc_start: 0.7779 (m110) cc_final: 0.7408 (m-40) REVERT: B 262 ASN cc_start: 0.7917 (t0) cc_final: 0.7661 (t0) REVERT: B 321 ARG cc_start: 0.6718 (mtm-85) cc_final: 0.6079 (mtp-110) REVERT: B 325 GLU cc_start: 0.6945 (tt0) cc_final: 0.6427 (pt0) REVERT: B 330 TYR cc_start: 0.7018 (OUTLIER) cc_final: 0.5637 (t80) REVERT: B 341 THR cc_start: 0.7523 (p) cc_final: 0.6676 (p) REVERT: B 363 LYS cc_start: 0.7424 (mtpp) cc_final: 0.6875 (mmtm) REVERT: B 485 GLU cc_start: 0.7879 (OUTLIER) cc_final: 0.7627 (mm-30) REVERT: C 19 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.5778 (mm-40) REVERT: C 58 GLU cc_start: 0.6979 (mp0) cc_final: 0.6746 (OUTLIER) REVERT: C 156 ARG cc_start: 0.8873 (OUTLIER) cc_final: 0.8354 (mtp85) REVERT: C 262 ASN cc_start: 0.8317 (t0) cc_final: 0.8092 (t0) REVERT: C 321 ARG cc_start: 0.6717 (mtm-85) cc_final: 0.6119 (mtp-110) REVERT: C 325 GLU cc_start: 0.6711 (tt0) cc_final: 0.6249 (pt0) REVERT: C 347 ASP cc_start: 0.7956 (p0) cc_final: 0.7671 (p0) REVERT: C 399 GLU cc_start: 0.8336 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: C 409 MET cc_start: 0.8282 (mtp) cc_final: 0.7649 (mtm) REVERT: C 438 ASP cc_start: 0.6420 (m-30) cc_final: 0.5914 (t0) REVERT: C 484 HIS cc_start: 0.7285 (m170) cc_final: 0.7028 (m170) REVERT: D 19 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.5861 (mm-40) REVERT: D 102 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7409 (tt) REVERT: D 156 ARG cc_start: 0.8889 (OUTLIER) cc_final: 0.8315 (mtp85) REVERT: D 321 ARG cc_start: 0.7193 (mpt180) cc_final: 0.6786 (mpt90) REVERT: D 349 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: D 409 MET cc_start: 0.8239 (mtp) cc_final: 0.7633 (mtm) REVERT: D 438 ASP cc_start: 0.6239 (m-30) cc_final: 0.5795 (t0) outliers start: 77 outliers final: 49 residues processed: 275 average time/residue: 1.1625 time to fit residues: 355.6449 Evaluate side-chains 289 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 226 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 58 GLU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 464 CYS Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 109 optimal weight: 2.9990 chunk 2 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 0.1980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 171 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 162 optimal weight: 0.7980 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 301 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.158559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.139039 restraints weight = 18082.913| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 1.96 r_work: 0.3721 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3618 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 15748 Z= 0.174 Angle : 0.533 5.918 21352 Z= 0.286 Chirality : 0.043 0.167 2364 Planarity : 0.004 0.038 2736 Dihedral : 7.821 57.935 2342 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.90 % Allowed : 16.86 % Favored : 78.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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 (0.20), residues: 1964 helix: 1.40 (0.18), residues: 860 sheet: -0.09 (0.26), residues: 420 loop : -0.44 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP C 178 HIS 0.008 0.001 HIS D 484 PHE 0.012 0.001 PHE D 411 TYR 0.021 0.002 TYR B 351 ARG 0.004 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04278 ( 797) hydrogen bonds : angle 4.78431 ( 2283) covalent geometry : bond 0.00419 (15748) covalent geometry : angle 0.53301 (21352) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 227 time to evaluate : 1.809 Fit side-chains REVERT: A 19 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.5959 (mm-40) REVERT: A 58 GLU cc_start: 0.6947 (mp0) cc_final: 0.6609 (pm20) REVERT: A 156 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8368 (mtp85) REVERT: A 321 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6145 (mtp-110) REVERT: A 325 GLU cc_start: 0.6877 (tt0) cc_final: 0.6368 (pt0) REVERT: A 349 GLU cc_start: 0.6817 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: A 399 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8012 (mt-10) REVERT: A 409 MET cc_start: 0.8291 (mtp) cc_final: 0.7716 (mtm) REVERT: B 19 GLN cc_start: 0.7069 (OUTLIER) cc_final: 0.6084 (mm-40) REVERT: B 121 ASN cc_start: 0.7807 (m110) cc_final: 0.7392 (m-40) REVERT: B 262 ASN cc_start: 0.7948 (t0) cc_final: 0.7710 (t0) REVERT: B 321 ARG cc_start: 0.6741 (mtm-85) cc_final: 0.6091 (mtp-110) REVERT: B 325 GLU cc_start: 0.6964 (tt0) cc_final: 0.6443 (pt0) REVERT: B 330 TYR cc_start: 0.7050 (OUTLIER) cc_final: 0.5500 (t80) REVERT: B 341 THR cc_start: 0.7556 (p) cc_final: 0.6625 (p) REVERT: B 485 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: C 19 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5840 (mm-40) REVERT: C 58 GLU cc_start: 0.7018 (mp0) cc_final: 0.6754 (OUTLIER) REVERT: C 102 LEU cc_start: 0.7663 (OUTLIER) cc_final: 0.7336 (tt) REVERT: C 121 ASN cc_start: 0.7728 (m110) cc_final: 0.7490 (m-40) REVERT: C 156 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8364 (mtp85) REVERT: C 262 ASN cc_start: 0.8339 (t0) cc_final: 0.8099 (t0) REVERT: C 321 ARG cc_start: 0.6732 (mtm-85) cc_final: 0.6115 (mtp-110) REVERT: C 325 GLU cc_start: 0.6744 (tt0) cc_final: 0.6238 (pt0) REVERT: C 347 ASP cc_start: 0.7973 (p0) cc_final: 0.7683 (p0) REVERT: C 399 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8055 (mt-10) REVERT: C 409 MET cc_start: 0.8364 (mtp) cc_final: 0.7731 (mtm) REVERT: C 438 ASP cc_start: 0.6460 (m-30) cc_final: 0.5935 (t0) REVERT: C 484 HIS cc_start: 0.7295 (m170) cc_final: 0.7032 (m170) REVERT: D 19 GLN cc_start: 0.7142 (OUTLIER) cc_final: 0.5982 (mm-40) REVERT: D 58 GLU cc_start: 0.6532 (mp0) cc_final: 0.6080 (mp0) REVERT: D 102 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7412 (tt) REVERT: D 156 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8310 (mtp85) REVERT: D 349 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6381 (mp0) REVERT: D 409 MET cc_start: 0.8266 (mtp) cc_final: 0.7656 (mtm) REVERT: D 438 ASP cc_start: 0.6240 (m-30) cc_final: 0.5798 (t0) outliers start: 80 outliers final: 44 residues processed: 275 average time/residue: 1.2087 time to fit residues: 371.4505 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 222 time to evaluate : 1.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 5.9990 chunk 70 optimal weight: 0.2980 chunk 136 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 192 optimal weight: 2.9990 chunk 191 optimal weight: 1.9990 chunk 104 optimal weight: 0.6980 chunk 190 optimal weight: 0.6980 chunk 63 optimal weight: 0.7980 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3918 r_free = 0.3918 target = 0.158342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.138588 restraints weight = 17894.401| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 2.00 r_work: 0.3680 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15748 Z= 0.118 Angle : 0.492 6.366 21352 Z= 0.264 Chirality : 0.042 0.165 2364 Planarity : 0.004 0.038 2736 Dihedral : 7.472 58.035 2340 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.56 % Allowed : 18.09 % Favored : 78.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.20), residues: 1964 helix: 1.53 (0.18), residues: 860 sheet: -0.01 (0.26), residues: 420 loop : -0.41 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 178 HIS 0.008 0.001 HIS D 484 PHE 0.010 0.001 PHE B 411 TYR 0.019 0.001 TYR B 351 ARG 0.004 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03662 ( 797) hydrogen bonds : angle 4.68204 ( 2283) covalent geometry : bond 0.00270 (15748) covalent geometry : angle 0.49187 (21352) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 230 time to evaluate : 1.736 Fit side-chains REVERT: A 19 GLN cc_start: 0.7020 (OUTLIER) cc_final: 0.5790 (mm-40) REVERT: A 156 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.8325 (mtp85) REVERT: A 321 ARG cc_start: 0.6766 (mtm-85) cc_final: 0.6121 (mtp-110) REVERT: A 325 GLU cc_start: 0.6854 (tt0) cc_final: 0.6342 (pt0) REVERT: A 399 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8023 (mt-10) REVERT: A 409 MET cc_start: 0.8224 (mtp) cc_final: 0.7648 (mtm) REVERT: B 19 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.5956 (mm-40) REVERT: B 121 ASN cc_start: 0.7800 (m110) cc_final: 0.7408 (m-40) REVERT: B 262 ASN cc_start: 0.7907 (t0) cc_final: 0.7625 (t0) REVERT: B 321 ARG cc_start: 0.6721 (mtm-85) cc_final: 0.6083 (mtp-110) REVERT: B 325 GLU cc_start: 0.6970 (tt0) cc_final: 0.6434 (pt0) REVERT: B 330 TYR cc_start: 0.7049 (OUTLIER) cc_final: 0.5415 (t80) REVERT: B 341 THR cc_start: 0.7492 (p) cc_final: 0.6515 (p) REVERT: B 363 LYS cc_start: 0.7338 (mtpp) cc_final: 0.6687 (mmtm) REVERT: B 485 GLU cc_start: 0.7760 (OUTLIER) cc_final: 0.7506 (mm-30) REVERT: C 19 GLN cc_start: 0.7003 (OUTLIER) cc_final: 0.5743 (mm-40) REVERT: C 58 GLU cc_start: 0.7044 (mp0) cc_final: 0.6812 (OUTLIER) REVERT: C 102 LEU cc_start: 0.7575 (OUTLIER) cc_final: 0.7233 (tt) REVERT: C 156 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8352 (mtp85) REVERT: C 262 ASN cc_start: 0.8332 (t0) cc_final: 0.8108 (t0) REVERT: C 321 ARG cc_start: 0.6710 (mtm-85) cc_final: 0.6099 (mtp-110) REVERT: C 325 GLU cc_start: 0.6676 (tt0) cc_final: 0.6219 (pt0) REVERT: C 399 GLU cc_start: 0.8315 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: C 409 MET cc_start: 0.8290 (mtp) cc_final: 0.7645 (mtm) REVERT: C 438 ASP cc_start: 0.6184 (m-30) cc_final: 0.5734 (t0) REVERT: C 484 HIS cc_start: 0.7289 (m170) cc_final: 0.7025 (m170) REVERT: D 19 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5869 (mm-40) REVERT: D 102 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7318 (tt) REVERT: D 156 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8288 (mtp85) REVERT: D 409 MET cc_start: 0.8160 (mtp) cc_final: 0.7565 (mtm) REVERT: D 438 ASP cc_start: 0.6164 (m-30) cc_final: 0.5676 (t0) REVERT: D 485 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.6512 (mp0) outliers start: 58 outliers final: 34 residues processed: 265 average time/residue: 1.1300 time to fit residues: 334.3598 Evaluate side-chains 270 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 223 time to evaluate : 1.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 464 CYS Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 190 optimal weight: 0.7980 chunk 156 optimal weight: 0.7980 chunk 115 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 350 GLN C 301 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.156806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136836 restraints weight = 17794.331| |-----------------------------------------------------------------------------| r_work (start): 0.3740 rms_B_bonded: 2.04 r_work: 0.3657 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3552 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3552 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7380 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15748 Z= 0.163 Angle : 0.702 42.576 21352 Z= 0.345 Chirality : 0.043 0.168 2364 Planarity : 0.004 0.066 2736 Dihedral : 7.552 59.159 2340 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.41 % Allowed : 17.66 % Favored : 77.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.62 (0.20), residues: 1964 helix: 1.44 (0.18), residues: 860 sheet: -0.09 (0.26), residues: 420 loop : -0.46 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 178 HIS 0.010 0.001 HIS D 484 PHE 0.012 0.001 PHE D 411 TYR 0.020 0.002 TYR B 351 ARG 0.003 0.000 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04080 ( 797) hydrogen bonds : angle 4.73049 ( 2283) covalent geometry : bond 0.00395 (15748) covalent geometry : angle 0.70152 (21352) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 298 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 226 time to evaluate : 1.852 Fit side-chains REVERT: A 19 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.5820 (mm-40) REVERT: A 58 GLU cc_start: 0.6875 (mp0) cc_final: 0.6567 (mt-10) REVERT: A 156 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8299 (mtp85) REVERT: A 321 ARG cc_start: 0.6764 (mtm-85) cc_final: 0.6120 (mtp-110) REVERT: A 325 GLU cc_start: 0.6846 (tt0) cc_final: 0.6330 (pt0) REVERT: A 349 GLU cc_start: 0.6836 (OUTLIER) cc_final: 0.6335 (mp0) REVERT: A 399 GLU cc_start: 0.8313 (OUTLIER) cc_final: 0.8038 (mt-10) REVERT: A 409 MET cc_start: 0.8343 (mtp) cc_final: 0.7746 (mtm) REVERT: A 485 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 19 GLN cc_start: 0.7026 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: B 121 ASN cc_start: 0.7720 (m110) cc_final: 0.7265 (m-40) REVERT: B 262 ASN cc_start: 0.7951 (t0) cc_final: 0.7666 (t0) REVERT: B 321 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6105 (mtp-110) REVERT: B 325 GLU cc_start: 0.6953 (tt0) cc_final: 0.6433 (pt0) REVERT: B 330 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5493 (t80) REVERT: B 341 THR cc_start: 0.7671 (p) cc_final: 0.6685 (p) REVERT: B 363 LYS cc_start: 0.7380 (mtpp) cc_final: 0.6724 (mmtm) REVERT: B 485 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7535 (mm-30) REVERT: C 19 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.5775 (mm-40) REVERT: C 58 GLU cc_start: 0.7065 (mp0) cc_final: 0.6824 (OUTLIER) REVERT: C 102 LEU cc_start: 0.7591 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 156 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8333 (mtp85) REVERT: C 262 ASN cc_start: 0.8389 (t0) cc_final: 0.8169 (t0) REVERT: C 321 ARG cc_start: 0.6723 (mtm-85) cc_final: 0.6120 (mtp-110) REVERT: C 325 GLU cc_start: 0.6664 (tt0) cc_final: 0.6197 (pt0) REVERT: C 349 GLU cc_start: 0.6761 (OUTLIER) cc_final: 0.6144 (mp0) REVERT: C 399 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: C 409 MET cc_start: 0.8312 (mtp) cc_final: 0.7665 (mtm) REVERT: C 438 ASP cc_start: 0.6399 (m-30) cc_final: 0.5901 (t0) REVERT: C 484 HIS cc_start: 0.7293 (m170) cc_final: 0.7044 (m170) REVERT: D 19 GLN cc_start: 0.7128 (OUTLIER) cc_final: 0.5888 (mm-40) REVERT: D 102 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7329 (tt) REVERT: D 156 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8324 (mtp85) REVERT: D 349 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6377 (mp0) REVERT: D 399 GLU cc_start: 0.8369 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 409 MET cc_start: 0.8222 (mtp) cc_final: 0.7612 (mtm) REVERT: D 438 ASP cc_start: 0.6222 (m-30) cc_final: 0.5757 (t0) outliers start: 72 outliers final: 44 residues processed: 270 average time/residue: 1.2168 time to fit residues: 364.7594 Evaluate side-chains 283 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 222 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain A residue 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 165 optimal weight: 0.9980 chunk 81 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 140 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 350 GLN C 69 GLN C 301 GLN D 69 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.156948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.137035 restraints weight = 17815.870| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.03 r_work: 0.3668 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15748 Z= 0.152 Angle : 0.520 6.368 21352 Z= 0.279 Chirality : 0.043 0.167 2364 Planarity : 0.004 0.037 2736 Dihedral : 7.532 59.872 2340 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.05 % Allowed : 18.15 % Favored : 77.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.20), residues: 1964 helix: 1.48 (0.18), residues: 856 sheet: -0.08 (0.26), residues: 420 loop : -0.46 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.011 0.001 HIS B 484 PHE 0.012 0.001 PHE B 411 TYR 0.020 0.002 TYR B 351 ARG 0.003 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03997 ( 797) hydrogen bonds : angle 4.71602 ( 2283) covalent geometry : bond 0.00364 (15748) covalent geometry : angle 0.51994 (21352) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 1.761 Fit side-chains REVERT: A 19 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.5813 (mm-40) REVERT: A 156 ARG cc_start: 0.8843 (OUTLIER) cc_final: 0.8243 (mtp85) REVERT: A 321 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6114 (mtp-110) REVERT: A 325 GLU cc_start: 0.6845 (tt0) cc_final: 0.6343 (pt0) REVERT: A 399 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8029 (mt-10) REVERT: A 409 MET cc_start: 0.8347 (mtp) cc_final: 0.7751 (mtm) REVERT: B 19 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.5887 (mm-40) REVERT: B 262 ASN cc_start: 0.7942 (t0) cc_final: 0.7665 (t0) REVERT: B 321 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6090 (mtp-110) REVERT: B 325 GLU cc_start: 0.6988 (tt0) cc_final: 0.6463 (pt0) REVERT: B 330 TYR cc_start: 0.7063 (OUTLIER) cc_final: 0.5465 (t80) REVERT: B 341 THR cc_start: 0.7529 (p) cc_final: 0.6540 (p) REVERT: B 363 LYS cc_start: 0.7417 (mtpp) cc_final: 0.6767 (mmtm) REVERT: B 460 VAL cc_start: 0.7661 (m) cc_final: 0.7428 (m) REVERT: B 485 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7544 (mm-30) REVERT: C 19 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.5778 (mm-40) REVERT: C 58 GLU cc_start: 0.7068 (mp0) cc_final: 0.6832 (OUTLIER) REVERT: C 102 LEU cc_start: 0.7589 (OUTLIER) cc_final: 0.7257 (tt) REVERT: C 156 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8281 (mtp85) REVERT: C 262 ASN cc_start: 0.8384 (t0) cc_final: 0.8163 (t0) REVERT: C 321 ARG cc_start: 0.6714 (mtm-85) cc_final: 0.6120 (mtp-110) REVERT: C 325 GLU cc_start: 0.6677 (tt0) cc_final: 0.6216 (pt0) REVERT: C 349 GLU cc_start: 0.6783 (OUTLIER) cc_final: 0.6168 (mp0) REVERT: C 399 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 409 MET cc_start: 0.8312 (mtp) cc_final: 0.7660 (mtm) REVERT: C 438 ASP cc_start: 0.6381 (m-30) cc_final: 0.5884 (t0) REVERT: C 484 HIS cc_start: 0.7323 (m170) cc_final: 0.7051 (m170) REVERT: D 19 GLN cc_start: 0.7100 (OUTLIER) cc_final: 0.5862 (mm-40) REVERT: D 102 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7323 (tt) REVERT: D 156 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8306 (mtp85) REVERT: D 349 GLU cc_start: 0.6864 (OUTLIER) cc_final: 0.6376 (mp0) REVERT: D 399 GLU cc_start: 0.8362 (OUTLIER) cc_final: 0.8129 (mt-10) REVERT: D 409 MET cc_start: 0.8228 (mtp) cc_final: 0.7608 (mtm) REVERT: D 438 ASP cc_start: 0.6206 (m-30) cc_final: 0.5749 (t0) outliers start: 66 outliers final: 42 residues processed: 267 average time/residue: 1.1933 time to fit residues: 353.9391 Evaluate side-chains 275 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 218 time to evaluate : 1.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain B residue 485 GLU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 173 optimal weight: 0.7980 chunk 57 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 138 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 186 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 350 GLN C 69 GLN D 69 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.157047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.137112 restraints weight = 17942.914| |-----------------------------------------------------------------------------| r_work (start): 0.3750 rms_B_bonded: 2.04 r_work: 0.3667 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7375 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 15748 Z= 0.151 Angle : 0.522 6.266 21352 Z= 0.280 Chirality : 0.043 0.167 2364 Planarity : 0.004 0.037 2736 Dihedral : 7.496 58.300 2340 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.11 % Allowed : 18.33 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.65 (0.20), residues: 1964 helix: 1.45 (0.18), residues: 860 sheet: -0.07 (0.26), residues: 420 loop : -0.43 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 178 HIS 0.013 0.001 HIS D 484 PHE 0.012 0.001 PHE B 411 TYR 0.020 0.002 TYR B 351 ARG 0.003 0.000 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.03994 ( 797) hydrogen bonds : angle 4.72150 ( 2283) covalent geometry : bond 0.00364 (15748) covalent geometry : angle 0.52224 (21352) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3928 Ramachandran restraints generated. 1964 Oldfield, 0 Emsley, 1964 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 216 time to evaluate : 1.675 Fit side-chains REVERT: A 19 GLN cc_start: 0.7090 (OUTLIER) cc_final: 0.5829 (mm-40) REVERT: A 156 ARG cc_start: 0.8844 (OUTLIER) cc_final: 0.8258 (mtp85) REVERT: A 321 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6136 (mtp-110) REVERT: A 325 GLU cc_start: 0.6897 (tt0) cc_final: 0.6351 (pt0) REVERT: A 399 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8032 (mt-10) REVERT: A 409 MET cc_start: 0.8337 (mtp) cc_final: 0.7738 (mtm) REVERT: B 19 GLN cc_start: 0.7030 (OUTLIER) cc_final: 0.5864 (mm-40) REVERT: B 121 ASN cc_start: 0.7752 (m110) cc_final: 0.7326 (m-40) REVERT: B 262 ASN cc_start: 0.7949 (t0) cc_final: 0.7679 (t0) REVERT: B 321 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6082 (mtp-110) REVERT: B 325 GLU cc_start: 0.7016 (tt0) cc_final: 0.6440 (pt0) REVERT: B 330 TYR cc_start: 0.7134 (OUTLIER) cc_final: 0.5409 (t80) REVERT: B 341 THR cc_start: 0.7545 (p) cc_final: 0.6474 (p) REVERT: B 363 LYS cc_start: 0.7420 (mtpp) cc_final: 0.6765 (mmtm) REVERT: B 460 VAL cc_start: 0.7661 (m) cc_final: 0.7422 (m) REVERT: C 19 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5793 (mm-40) REVERT: C 58 GLU cc_start: 0.7099 (mp0) cc_final: 0.6822 (OUTLIER) REVERT: C 102 LEU cc_start: 0.7580 (OUTLIER) cc_final: 0.7250 (tt) REVERT: C 156 ARG cc_start: 0.8882 (OUTLIER) cc_final: 0.8319 (mtp85) REVERT: C 262 ASN cc_start: 0.8387 (t0) cc_final: 0.8165 (t0) REVERT: C 321 ARG cc_start: 0.6737 (mtm-85) cc_final: 0.6121 (mtp-110) REVERT: C 325 GLU cc_start: 0.6687 (tt0) cc_final: 0.6222 (pt0) REVERT: C 349 GLU cc_start: 0.6803 (OUTLIER) cc_final: 0.6186 (mp0) REVERT: C 399 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8089 (mt-10) REVERT: C 409 MET cc_start: 0.8321 (mtp) cc_final: 0.7668 (mtm) REVERT: C 438 ASP cc_start: 0.6336 (m-30) cc_final: 0.5964 (t0) REVERT: C 484 HIS cc_start: 0.7322 (m170) cc_final: 0.7046 (m170) REVERT: D 19 GLN cc_start: 0.7105 (OUTLIER) cc_final: 0.5834 (mm-40) REVERT: D 102 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7312 (tt) REVERT: D 156 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8263 (mtp85) REVERT: D 349 GLU cc_start: 0.6859 (OUTLIER) cc_final: 0.6371 (mp0) REVERT: D 399 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: D 409 MET cc_start: 0.8236 (mtp) cc_final: 0.7610 (mtm) REVERT: D 438 ASP cc_start: 0.6179 (m-30) cc_final: 0.5697 (t0) outliers start: 67 outliers final: 45 residues processed: 261 average time/residue: 1.2819 time to fit residues: 371.9611 Evaluate side-chains 272 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 213 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 73 ILE Chi-restraints excluded: chain C residue 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 349 GLU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 35 optimal weight: 2.9990 chunk 185 optimal weight: 0.8980 chunk 124 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 73 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 176 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 350 GLN B 474 ASN C 69 GLN C 301 GLN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.156846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136910 restraints weight = 17842.094| |-----------------------------------------------------------------------------| r_work (start): 0.3742 rms_B_bonded: 2.04 r_work: 0.3659 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 15748 Z= 0.183 Angle : 0.933 61.592 21352 Z= 0.457 Chirality : 0.044 0.370 2364 Planarity : 0.004 0.037 2736 Dihedral : 7.524 58.373 2340 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.51 % Favored : 96.38 % Rotamer: Outliers : 3.99 % Allowed : 18.45 % Favored : 77.56 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % 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: 0.63 (0.20), residues: 1964 helix: 1.42 (0.18), residues: 860 sheet: -0.06 (0.26), residues: 420 loop : -0.44 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 178 HIS 0.013 0.001 HIS D 484 PHE 0.012 0.001 PHE B 411 TYR 0.019 0.002 TYR B 351 ARG 0.005 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 797) hydrogen bonds : angle 4.71558 ( 2283) covalent geometry : bond 0.00425 (15748) covalent geometry : angle 0.93298 (21352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10823.43 seconds wall clock time: 187 minutes 17.78 seconds (11237.78 seconds total)