Starting phenix.real_space_refine on Sat Jun 14 00:46:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ene_28271/06_2025/8ene_28271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ene_28271/06_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_28271/06_2025/8ene_28271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ene_28271/06_2025/8ene_28271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ene_28271/06_2025/8ene_28271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ene_28271/06_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/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: 8.78, per 1000 atoms: 0.57 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: 3.46 Conformation dependent library (CDL) restraints added in 1.9 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: 2.48 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: 6.80 Time building geometry restraints manager: 4.14 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: 1.560 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: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 35.980 Find NCS groups from input model: 0.740 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.360 ------------------------------------------------------------------------------- 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 : 1.892 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: 1.3294 time to fit residues: 541.7660 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 : 2.306 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.138402 restraints weight = 17903.103| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 2.02 r_work: 0.3677 rms_B_bonded: 2.38 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 5.00751 ( 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 : 3.777 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: 0.7043 (mp0) cc_final: 0.6840 (pm20) REVERT: A 87 ARG cc_start: 0.7968 (tpt90) cc_final: 0.7743 (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: 0.7129 (p0) REVERT: A 325 GLU cc_start: 0.6895 (tt0) cc_final: 0.6407 (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: 0.7872 (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: 0.6122 (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: 0.7201 (OUTLIER) cc_final: 0.6046 (t80) REVERT: B 341 THR cc_start: 0.7387 (p) cc_final: 0.6740 (p) REVERT: B 363 LYS cc_start: 0.7404 (mtpp) cc_final: 0.6783 (mmtm) REVERT: C 13 LEU cc_start: 0.5006 (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: 0.6931 (m170) REVERT: D 19 GLN cc_start: 0.7027 (OUTLIER) cc_final: 0.6097 (mm-40) REVERT: D 58 GLU cc_start: 0.7017 (mp0) cc_final: 0.6805 (pm20) REVERT: D 87 ARG cc_start: 0.7944 (tpt90) cc_final: 0.7735 (mmm160) REVERT: D 102 LEU cc_start: 0.7593 (OUTLIER) cc_final: 0.7270 (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: 0.7437 (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: 1.2588 time to fit residues: 391.0250 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 : 1.725 ------------------------------------------------------------------------------- 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: 1.9990 chunk 91 optimal weight: 4.9990 chunk 52 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 128 optimal weight: 0.9990 chunk 118 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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 = 0.3935 r_free = 0.3935 target = 0.157371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3745 r_free = 0.3745 target = 0.137640 restraints weight = 18085.044| |-----------------------------------------------------------------------------| r_work (start): 0.3791 rms_B_bonded: 1.98 r_work: 0.3710 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7420 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 15748 Z= 0.213 Angle : 0.580 7.679 21352 Z= 0.310 Chirality : 0.045 0.165 2364 Planarity : 0.005 0.042 2736 Dihedral : 8.725 58.471 2344 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.54 % Allowed : 16.43 % Favored : 79.03 % 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: 0.48 (0.19), residues: 1964 helix: 1.24 (0.18), residues: 864 sheet: -0.05 (0.25), residues: 420 loop : -0.51 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 178 HIS 0.006 0.001 HIS B 484 PHE 0.014 0.002 PHE C 24 TYR 0.023 0.002 TYR B 351 ARG 0.004 0.001 ARG A 131 Details of bonding type rmsd hydrogen bonds : bond 0.04918 ( 797) hydrogen bonds : angle 4.98827 ( 2283) covalent geometry : bond 0.00520 (15748) covalent geometry : angle 0.58034 (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 308 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 234 time to evaluate : 2.077 Fit side-chains REVERT: A 19 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.6018 (mm-40) REVERT: A 156 ARG cc_start: 0.8937 (OUTLIER) cc_final: 0.8373 (mtp85) REVERT: A 321 ARG cc_start: 0.6818 (mtm-85) cc_final: 0.6134 (mtp-110) REVERT: A 325 GLU cc_start: 0.6835 (tt0) cc_final: 0.6371 (pt0) REVERT: A 399 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: A 409 MET cc_start: 0.8293 (mtp) cc_final: 0.7679 (mtm) REVERT: B 19 GLN cc_start: 0.7060 (OUTLIER) cc_final: 0.6112 (mm-40) REVERT: B 121 ASN cc_start: 0.7813 (m110) cc_final: 0.7365 (m-40) REVERT: B 262 ASN cc_start: 0.8006 (t0) cc_final: 0.7791 (t0) REVERT: B 321 ARG cc_start: 0.6753 (mtm-85) cc_final: 0.6072 (mtp-110) REVERT: B 325 GLU cc_start: 0.6908 (tt0) cc_final: 0.6380 (pt0) REVERT: B 330 TYR cc_start: 0.7224 (OUTLIER) cc_final: 0.5943 (t80) REVERT: B 341 THR cc_start: 0.7502 (p) cc_final: 0.6837 (p) REVERT: B 416 ASP cc_start: 0.5701 (t70) cc_final: 0.5431 (m-30) REVERT: C 19 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.5857 (mm-40) REVERT: C 156 ARG cc_start: 0.8925 (OUTLIER) cc_final: 0.8354 (mtp85) REVERT: C 262 ASN cc_start: 0.8296 (t0) cc_final: 0.8087 (t0) REVERT: C 321 ARG cc_start: 0.6807 (mtm-85) cc_final: 0.6179 (mtp-110) REVERT: C 325 GLU cc_start: 0.6751 (tt0) cc_final: 0.6284 (pt0) REVERT: C 329 LYS cc_start: 0.7635 (mtpt) cc_final: 0.7372 (mtpt) REVERT: C 399 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: C 409 MET cc_start: 0.8360 (mtp) cc_final: 0.7716 (mtm) REVERT: C 481 TYR cc_start: 0.7011 (t80) cc_final: 0.6465 (t80) REVERT: C 485 GLU cc_start: 0.8029 (OUTLIER) cc_final: 0.6857 (mp0) REVERT: D 19 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.6113 (mm-40) REVERT: D 102 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7315 (tt) REVERT: D 156 ARG cc_start: 0.8955 (OUTLIER) cc_final: 0.8396 (mtp85) REVERT: D 349 GLU cc_start: 0.6872 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: D 409 MET cc_start: 0.8289 (mtp) cc_final: 0.7668 (mtm) REVERT: D 441 ILE cc_start: 0.7359 (mm) cc_final: 0.7124 (mm) REVERT: D 481 TYR cc_start: 0.7006 (t80) cc_final: 0.6501 (t80) REVERT: D 485 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.6662 (mp0) outliers start: 74 outliers final: 37 residues processed: 278 average time/residue: 1.3129 time to fit residues: 403.9127 Evaluate side-chains 273 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 222 time to evaluate : 1.757 ------------------------------------------------------------------------------- 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 415 ASP Chi-restraints excluded: chain A residue 417 VAL 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 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 415 ASP Chi-restraints excluded: chain C residue 461 SER 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 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 Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 176 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 137 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 190 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 162 optimal weight: 1.9990 chunk 114 optimal weight: 0.4980 chunk 49 optimal weight: 4.9990 chunk 18 optimal weight: 0.9980 chunk 124 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3908 r_free = 0.3908 target = 0.157459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137807 restraints weight = 17798.446| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.99 r_work: 0.3668 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3564 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15748 Z= 0.128 Angle : 0.505 6.264 21352 Z= 0.271 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.040 2736 Dihedral : 7.945 58.317 2340 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.54 % Allowed : 16.86 % Favored : 78.60 % 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: 0.64 (0.20), residues: 1964 helix: 1.44 (0.18), residues: 860 sheet: -0.02 (0.26), residues: 420 loop : -0.49 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 178 HIS 0.006 0.001 HIS B 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 0.03942 ( 797) hydrogen bonds : angle 4.79837 ( 2283) covalent geometry : bond 0.00295 (15748) covalent geometry : angle 0.50500 (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 304 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 230 time to evaluate : 1.902 Fit side-chains REVERT: A 19 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.5904 (mm-40) REVERT: A 87 ARG cc_start: 0.7961 (tpt90) cc_final: 0.7754 (mmm160) REVERT: A 156 ARG cc_start: 0.8874 (OUTLIER) cc_final: 0.8337 (mtp85) REVERT: A 321 ARG cc_start: 0.6763 (mtm-85) cc_final: 0.6123 (mtp-110) REVERT: A 325 GLU cc_start: 0.6792 (tt0) cc_final: 0.6310 (pt0) REVERT: A 349 GLU cc_start: 0.6762 (OUTLIER) cc_final: 0.6296 (mp0) REVERT: A 399 GLU cc_start: 0.8299 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: A 409 MET cc_start: 0.8232 (mtp) cc_final: 0.7624 (mtm) REVERT: B 19 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.6074 (mm-40) REVERT: B 121 ASN cc_start: 0.7822 (m110) cc_final: 0.7424 (m-40) REVERT: B 262 ASN cc_start: 0.7955 (t0) cc_final: 0.7740 (t0) REVERT: B 321 ARG cc_start: 0.6772 (mtm-85) cc_final: 0.6126 (mtp-110) REVERT: B 325 GLU cc_start: 0.6862 (tt0) cc_final: 0.6342 (pt0) REVERT: B 330 TYR cc_start: 0.7147 (OUTLIER) cc_final: 0.5755 (t80) REVERT: B 341 THR cc_start: 0.7501 (p) cc_final: 0.6686 (p) REVERT: B 363 LYS cc_start: 0.7361 (mtpp) cc_final: 0.6727 (mmtm) REVERT: B 416 ASP cc_start: 0.5753 (t70) cc_final: 0.5441 (m-30) REVERT: C 19 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5774 (mm-40) REVERT: C 121 ASN cc_start: 0.7664 (m110) cc_final: 0.7397 (m-40) REVERT: C 156 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8355 (mtp85) REVERT: C 262 ASN cc_start: 0.8270 (t0) cc_final: 0.8017 (t0) REVERT: C 321 ARG cc_start: 0.6716 (mtm-85) cc_final: 0.6130 (mtp-110) REVERT: C 325 GLU cc_start: 0.6699 (tt0) cc_final: 0.6240 (pt0) REVERT: C 399 GLU cc_start: 0.8323 (OUTLIER) cc_final: 0.8086 (mt-10) REVERT: C 409 MET cc_start: 0.8224 (mtp) cc_final: 0.7590 (mtm) REVERT: C 438 ASP cc_start: 0.6446 (m-30) cc_final: 0.5876 (t0) REVERT: D 19 GLN cc_start: 0.7055 (OUTLIER) cc_final: 0.5926 (mm-40) REVERT: D 102 LEU cc_start: 0.7705 (OUTLIER) cc_final: 0.7365 (tt) REVERT: D 156 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8306 (mtp85) REVERT: D 409 MET cc_start: 0.8215 (mtp) cc_final: 0.7600 (mtm) REVERT: D 438 ASP cc_start: 0.6190 (m-30) cc_final: 0.5693 (t0) outliers start: 74 outliers final: 44 residues processed: 278 average time/residue: 1.3539 time to fit residues: 418.2048 Evaluate side-chains 277 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 221 time to evaluate : 1.630 ------------------------------------------------------------------------------- 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 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 357 LEU 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 B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN 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 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS 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 114 LEU 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 315 ILE Chi-restraints excluded: chain C residue 357 LEU 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 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 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 412 LYS 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 193 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 183 optimal weight: 3.9990 chunk 72 optimal weight: 1.9990 chunk 162 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 187 optimal weight: 0.9990 chunk 64 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 185 optimal weight: 2.9990 chunk 135 optimal weight: 0.5980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3917 r_free = 0.3917 target = 0.158349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.138662 restraints weight = 17833.410| |-----------------------------------------------------------------------------| r_work (start): 0.3767 rms_B_bonded: 1.98 r_work: 0.3685 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3583 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15748 Z= 0.120 Angle : 0.485 5.728 21352 Z= 0.261 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.039 2736 Dihedral : 7.655 58.037 2340 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.60 % Allowed : 17.11 % Favored : 78.30 % 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: 0.71 (0.20), residues: 1964 helix: 1.51 (0.18), residues: 860 sheet: -0.01 (0.26), residues: 420 loop : -0.44 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 178 HIS 0.007 0.001 HIS D 484 PHE 0.010 0.001 PHE D 290 TYR 0.020 0.001 TYR B 351 ARG 0.003 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 797) hydrogen bonds : angle 4.71670 ( 2283) covalent geometry : bond 0.00277 (15748) covalent geometry : angle 0.48490 (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 304 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 229 time to evaluate : 4.898 Fit side-chains REVERT: A 19 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5796 (mm-40) REVERT: A 109 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7053 (ttp) REVERT: A 156 ARG cc_start: 0.8855 (OUTLIER) cc_final: 0.8301 (mtp85) REVERT: A 321 ARG cc_start: 0.6736 (mtm-85) cc_final: 0.6107 (mtp-110) REVERT: A 325 GLU cc_start: 0.6838 (tt0) cc_final: 0.6288 (pt0) REVERT: A 349 GLU cc_start: 0.6774 (OUTLIER) cc_final: 0.6295 (mp0) REVERT: A 399 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: A 409 MET cc_start: 0.8225 (mtp) cc_final: 0.7633 (mtm) REVERT: B 19 GLN cc_start: 0.7000 (OUTLIER) cc_final: 0.6014 (mm-40) REVERT: B 109 MET cc_start: 0.7330 (OUTLIER) cc_final: 0.7046 (ttp) REVERT: B 262 ASN cc_start: 0.7923 (t0) cc_final: 0.7649 (t0) REVERT: B 321 ARG cc_start: 0.6749 (mtm-85) cc_final: 0.6123 (mtp-110) REVERT: B 325 GLU cc_start: 0.6868 (tt0) cc_final: 0.6359 (pt0) REVERT: B 330 TYR cc_start: 0.7069 (OUTLIER) cc_final: 0.5510 (t80) REVERT: B 341 THR cc_start: 0.7543 (p) cc_final: 0.6664 (p) REVERT: B 363 LYS cc_start: 0.7428 (mtpp) cc_final: 0.6825 (mmtm) REVERT: B 389 ASN cc_start: 0.7791 (m-40) cc_final: 0.7535 (m-40) REVERT: B 485 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7625 (mm-30) REVERT: C 19 GLN cc_start: 0.7009 (OUTLIER) cc_final: 0.5789 (mm-40) REVERT: C 156 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: C 262 ASN cc_start: 0.8327 (t0) cc_final: 0.8094 (t0) REVERT: C 321 ARG cc_start: 0.6708 (mtm-85) cc_final: 0.6122 (mtp-110) REVERT: C 325 GLU cc_start: 0.6699 (tt0) cc_final: 0.6257 (pt0) REVERT: C 399 GLU cc_start: 0.8341 (OUTLIER) cc_final: 0.8102 (mt-10) REVERT: C 409 MET cc_start: 0.8212 (mtp) cc_final: 0.7573 (mtm) REVERT: C 438 ASP cc_start: 0.6243 (m-30) cc_final: 0.5759 (t0) REVERT: D 19 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.5854 (mm-40) REVERT: D 102 LEU cc_start: 0.7710 (OUTLIER) cc_final: 0.7358 (tt) REVERT: D 156 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8242 (mtp85) REVERT: D 321 ARG cc_start: 0.7106 (mpt180) cc_final: 0.6755 (mpt90) REVERT: D 409 MET cc_start: 0.8192 (mtp) cc_final: 0.7569 (mtm) REVERT: D 438 ASP cc_start: 0.6147 (m-30) cc_final: 0.5659 (t0) outliers start: 75 outliers final: 44 residues processed: 274 average time/residue: 1.4850 time to fit residues: 454.5418 Evaluate side-chains 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 215 time to evaluate : 1.886 ------------------------------------------------------------------------------- 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 109 MET 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 357 LEU 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 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 109 MET 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 209 ILE 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 412 LYS 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 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 357 LEU 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 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 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 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: 6.9990 chunk 186 optimal weight: 3.9990 chunk 51 optimal weight: 0.0980 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 171 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 158 optimal weight: 3.9990 chunk 162 optimal weight: 0.5980 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 = 0.3871 r_free = 0.3871 target = 0.153875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.134265 restraints weight = 18060.329| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.98 r_work: 0.3630 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 15748 Z= 0.248 Angle : 0.604 7.153 21352 Z= 0.322 Chirality : 0.046 0.171 2364 Planarity : 0.005 0.043 2736 Dihedral : 8.054 59.730 2340 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.70 % Allowed : 16.86 % Favored : 77.44 % 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: 0.35 (0.19), residues: 1964 helix: 1.22 (0.18), residues: 856 sheet: -0.26 (0.25), residues: 420 loop : -0.58 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 453 HIS 0.007 0.002 HIS C 484 PHE 0.016 0.002 PHE C 24 TYR 0.023 0.002 TYR B 351 ARG 0.005 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04977 ( 797) hydrogen bonds : angle 4.95748 ( 2283) covalent geometry : bond 0.00612 (15748) covalent geometry : angle 0.60402 (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: 93 poor density : 214 time to evaluate : 1.633 Fit side-chains REVERT: A 19 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5935 (mm-40) REVERT: A 156 ARG cc_start: 0.8927 (OUTLIER) cc_final: 0.8377 (mtp85) REVERT: A 321 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6157 (mtp-110) REVERT: A 325 GLU cc_start: 0.6908 (tt0) cc_final: 0.6366 (pt0) REVERT: A 349 GLU cc_start: 0.6850 (OUTLIER) cc_final: 0.6566 (mp0) REVERT: A 399 GLU cc_start: 0.8327 (OUTLIER) cc_final: 0.8059 (mt-10) REVERT: B 19 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.5980 (mm-40) REVERT: B 121 ASN cc_start: 0.7758 (m110) cc_final: 0.7293 (m-40) REVERT: B 262 ASN cc_start: 0.8027 (t0) cc_final: 0.7808 (t0) REVERT: B 321 ARG cc_start: 0.6815 (mtm-85) cc_final: 0.6139 (mtp-110) REVERT: B 325 GLU cc_start: 0.6995 (tt0) cc_final: 0.6483 (pt0) REVERT: B 330 TYR cc_start: 0.7157 (OUTLIER) cc_final: 0.5332 (t80) REVERT: B 341 THR cc_start: 0.7646 (p) cc_final: 0.6659 (p) REVERT: B 349 GLU cc_start: 0.6856 (OUTLIER) cc_final: 0.6587 (mp0) REVERT: B 485 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7698 (mm-30) REVERT: C 19 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.5872 (mm-40) REVERT: C 102 LEU cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (tt) REVERT: C 156 ARG cc_start: 0.8936 (OUTLIER) cc_final: 0.8379 (mtp85) REVERT: C 262 ASN cc_start: 0.8426 (t0) cc_final: 0.8212 (t0) REVERT: C 321 ARG cc_start: 0.6789 (mtm-85) cc_final: 0.6152 (mtp-110) REVERT: C 325 GLU cc_start: 0.6756 (tt0) cc_final: 0.6248 (pt0) REVERT: C 349 GLU cc_start: 0.6882 (OUTLIER) cc_final: 0.6351 (mp0) REVERT: C 399 GLU cc_start: 0.8286 (OUTLIER) cc_final: 0.8041 (mt-10) REVERT: C 409 MET cc_start: 0.8366 (mtp) cc_final: 0.7710 (mtm) REVERT: C 485 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6619 (mp0) REVERT: D 19 GLN cc_start: 0.7161 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: D 102 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7253 (tt) REVERT: D 156 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8346 (mtp85) REVERT: D 349 GLU cc_start: 0.6956 (OUTLIER) cc_final: 0.6687 (mp0) REVERT: D 399 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8097 (mt-10) REVERT: D 438 ASP cc_start: 0.6260 (m-30) cc_final: 0.5796 (t0) REVERT: D 485 GLU cc_start: 0.7864 (OUTLIER) cc_final: 0.6595 (mp0) outliers start: 93 outliers final: 47 residues processed: 276 average time/residue: 1.2483 time to fit residues: 384.4843 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 213 time to evaluate : 1.649 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 220 ASN Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 320 VAL Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 357 LEU 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 349 GLU Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 412 LYS 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 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 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 C residue 485 GLU Chi-restraints excluded: chain C residue 488 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 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 357 LEU 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 485 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 170 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 136 optimal weight: 1.9990 chunk 73 optimal weight: 0.8980 chunk 58 optimal weight: 0.5980 chunk 3 optimal weight: 0.8980 chunk 192 optimal weight: 0.6980 chunk 191 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 190 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3913 r_free = 0.3913 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.138289 restraints weight = 17887.625| |-----------------------------------------------------------------------------| r_work (start): 0.3761 rms_B_bonded: 2.00 r_work: 0.3678 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3575 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 15748 Z= 0.116 Angle : 0.495 6.339 21352 Z= 0.267 Chirality : 0.042 0.163 2364 Planarity : 0.004 0.039 2736 Dihedral : 7.473 59.708 2338 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.17 % Allowed : 18.03 % 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: 0.63 (0.20), residues: 1964 helix: 1.44 (0.18), residues: 860 sheet: -0.06 (0.26), residues: 420 loop : -0.48 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 453 HIS 0.007 0.001 HIS C 484 PHE 0.011 0.001 PHE D 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 0.03619 ( 797) hydrogen bonds : angle 4.71580 ( 2283) covalent geometry : bond 0.00264 (15748) covalent geometry : angle 0.49536 (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 295 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 227 time to evaluate : 1.668 Fit side-chains REVERT: A 19 GLN cc_start: 0.7077 (OUTLIER) cc_final: 0.5828 (mm-40) REVERT: A 156 ARG cc_start: 0.8866 (OUTLIER) cc_final: 0.8280 (mtp85) REVERT: A 321 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6100 (mtp-110) REVERT: A 325 GLU cc_start: 0.6849 (tt0) cc_final: 0.6335 (pt0) REVERT: A 399 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8048 (mt-10) REVERT: A 409 MET cc_start: 0.8233 (mtp) cc_final: 0.7635 (mtm) REVERT: B 19 GLN cc_start: 0.6958 (OUTLIER) cc_final: 0.5839 (mm-40) REVERT: B 262 ASN cc_start: 0.7929 (t0) cc_final: 0.7700 (t0) REVERT: B 321 ARG cc_start: 0.6726 (mtm-85) cc_final: 0.6085 (mtp-110) REVERT: B 325 GLU cc_start: 0.6942 (tt0) cc_final: 0.6413 (pt0) REVERT: B 330 TYR cc_start: 0.7087 (OUTLIER) cc_final: 0.5570 (t80) REVERT: B 341 THR cc_start: 0.7647 (p) cc_final: 0.6664 (p) REVERT: B 363 LYS cc_start: 0.7349 (mtpp) cc_final: 0.6685 (mmtm) REVERT: B 389 ASN cc_start: 0.7768 (m-40) cc_final: 0.7505 (m-40) REVERT: C 19 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5872 (mm-40) REVERT: C 102 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7254 (tt) REVERT: C 156 ARG cc_start: 0.8884 (OUTLIER) cc_final: 0.8300 (mtp85) REVERT: C 262 ASN cc_start: 0.8382 (t0) cc_final: 0.8126 (t0) REVERT: C 321 ARG cc_start: 0.6691 (mtm-85) cc_final: 0.6085 (mtp-110) REVERT: C 325 GLU cc_start: 0.6675 (tt0) cc_final: 0.6220 (pt0) REVERT: C 399 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8078 (mt-10) REVERT: C 409 MET cc_start: 0.8296 (mtp) cc_final: 0.7639 (mtm) REVERT: C 438 ASP cc_start: 0.6186 (m-30) cc_final: 0.5713 (t0) REVERT: D 19 GLN cc_start: 0.7111 (OUTLIER) cc_final: 0.5878 (mm-40) REVERT: D 102 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7304 (tt) REVERT: D 156 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8308 (mtp85) REVERT: D 409 MET cc_start: 0.8222 (mtp) cc_final: 0.7640 (mtm) REVERT: D 438 ASP cc_start: 0.6154 (m-30) cc_final: 0.5668 (t0) outliers start: 68 outliers final: 41 residues processed: 270 average time/residue: 1.3039 time to fit residues: 392.4835 Evaluate side-chains 271 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 218 time to evaluate : 1.638 ------------------------------------------------------------------------------- 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 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER 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 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 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 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 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 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 73 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 172 optimal weight: 0.9980 chunk 190 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 115 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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 69 GLN B 350 GLN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3877 r_free = 0.3877 target = 0.154668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.134996 restraints weight = 17914.148| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 1.99 r_work: 0.3643 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3542 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7412 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 15748 Z= 0.211 Angle : 0.570 6.649 21352 Z= 0.305 Chirality : 0.045 0.168 2364 Planarity : 0.005 0.038 2736 Dihedral : 7.750 57.500 2338 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 5.15 % Allowed : 17.60 % Favored : 77.25 % 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: 0.41 (0.19), residues: 1964 helix: 1.28 (0.18), residues: 856 sheet: -0.21 (0.25), residues: 420 loop : -0.57 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP D 29 HIS 0.008 0.001 HIS C 484 PHE 0.014 0.002 PHE C 24 TYR 0.022 0.002 TYR B 351 ARG 0.004 0.001 ARG C 131 Details of bonding type rmsd hydrogen bonds : bond 0.04655 ( 797) hydrogen bonds : angle 4.88425 ( 2283) covalent geometry : bond 0.00516 (15748) covalent geometry : angle 0.56960 (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 297 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 213 time to evaluate : 1.584 Fit side-chains REVERT: A 19 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.5874 (mm-40) REVERT: A 156 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8323 (mtp85) REVERT: A 321 ARG cc_start: 0.6809 (mtm-85) cc_final: 0.6135 (mtp-110) REVERT: A 325 GLU cc_start: 0.6891 (tt0) cc_final: 0.6378 (pt0) REVERT: A 349 GLU cc_start: 0.6871 (OUTLIER) cc_final: 0.6384 (mp0) REVERT: A 399 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.8022 (mt-10) REVERT: A 409 MET cc_start: 0.8366 (mtp) cc_final: 0.7751 (mtm) REVERT: B 19 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.5981 (mm-40) REVERT: B 102 LEU cc_start: 0.7707 (OUTLIER) cc_final: 0.7386 (tt) REVERT: B 262 ASN cc_start: 0.8016 (t0) cc_final: 0.7805 (t0) REVERT: B 321 ARG cc_start: 0.6819 (mtm-85) cc_final: 0.6137 (mtp-110) REVERT: B 325 GLU cc_start: 0.7016 (tt0) cc_final: 0.6478 (pt0) REVERT: B 330 TYR cc_start: 0.7209 (OUTLIER) cc_final: 0.5400 (t80) REVERT: B 341 THR cc_start: 0.7664 (p) cc_final: 0.6493 (p) REVERT: C 19 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.5850 (mm-40) REVERT: C 102 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7325 (tt) REVERT: C 156 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8337 (mtp85) REVERT: C 262 ASN cc_start: 0.8433 (t0) cc_final: 0.8200 (t0) REVERT: C 321 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6146 (mtp-110) REVERT: C 325 GLU cc_start: 0.6671 (tt0) cc_final: 0.6241 (pt0) REVERT: C 399 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: C 409 MET cc_start: 0.8365 (mtp) cc_final: 0.7698 (mtm) REVERT: D 19 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.5893 (mm-40) REVERT: D 102 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7366 (tt) REVERT: D 156 ARG cc_start: 0.8899 (OUTLIER) cc_final: 0.8302 (mtp85) REVERT: D 399 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: D 409 MET cc_start: 0.8305 (mtp) cc_final: 0.7685 (mtm) REVERT: D 438 ASP cc_start: 0.6229 (m-30) cc_final: 0.5768 (t0) outliers start: 84 outliers final: 46 residues processed: 267 average time/residue: 1.3875 time to fit residues: 410.9083 Evaluate side-chains 268 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 207 time to evaluate : 3.990 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain A residue 220 ASN 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 357 LEU 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 488 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 102 LEU 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 220 ASN 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 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 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 320 VAL 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 488 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 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 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 357 LEU 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 Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 154 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 148 optimal weight: 2.9990 chunk 165 optimal weight: 0.8980 chunk 81 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 140 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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 69 GLN B 350 GLN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.156039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.136338 restraints weight = 17883.344| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 1.99 r_work: 0.3662 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7390 moved from start: 0.2184 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= 0.157 Angle : 0.535 6.601 21352 Z= 0.287 Chirality : 0.043 0.166 2364 Planarity : 0.004 0.039 2736 Dihedral : 7.615 58.714 2338 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.11 % Allowed : 18.64 % Favored : 77.25 % 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: 0.48 (0.19), residues: 1964 helix: 1.34 (0.18), residues: 856 sheet: -0.16 (0.25), residues: 420 loop : -0.56 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 29 HIS 0.011 0.002 HIS B 484 PHE 0.012 0.001 PHE B 411 TYR 0.020 0.002 TYR B 351 ARG 0.005 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.04173 ( 797) hydrogen bonds : angle 4.82226 ( 2283) covalent geometry : bond 0.00378 (15748) covalent geometry : angle 0.53459 (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 278 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 211 time to evaluate : 1.561 Fit side-chains REVERT: A 19 GLN cc_start: 0.7130 (OUTLIER) cc_final: 0.5857 (mm-40) REVERT: A 156 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8296 (mtp85) REVERT: A 321 ARG cc_start: 0.6778 (mtm-85) cc_final: 0.6115 (mtp-110) REVERT: A 325 GLU cc_start: 0.6861 (tt0) cc_final: 0.6356 (pt0) REVERT: A 399 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8056 (mt-10) REVERT: A 409 MET cc_start: 0.8336 (mtp) cc_final: 0.7733 (mtm) REVERT: B 19 GLN cc_start: 0.7065 (OUTLIER) cc_final: 0.5920 (mm-40) REVERT: B 102 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7348 (tt) REVERT: B 262 ASN cc_start: 0.7969 (t0) cc_final: 0.7766 (t0) REVERT: B 321 ARG cc_start: 0.6778 (mtm-85) cc_final: 0.6105 (mtp-110) REVERT: B 325 GLU cc_start: 0.7016 (tt0) cc_final: 0.6458 (pt0) REVERT: B 330 TYR cc_start: 0.7185 (OUTLIER) cc_final: 0.5297 (t80) REVERT: B 341 THR cc_start: 0.7655 (p) cc_final: 0.6397 (p) REVERT: B 363 LYS cc_start: 0.7480 (mtpp) cc_final: 0.6823 (mmtm) REVERT: C 19 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5895 (mm-40) REVERT: C 102 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7305 (tt) REVERT: C 156 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8325 (mtp85) REVERT: C 262 ASN cc_start: 0.8402 (t0) cc_final: 0.8149 (t0) REVERT: C 321 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6114 (mtp-110) REVERT: C 325 GLU cc_start: 0.6694 (tt0) cc_final: 0.6236 (pt0) REVERT: C 399 GLU cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mt-10) REVERT: C 409 MET cc_start: 0.8334 (mtp) cc_final: 0.7673 (mtm) REVERT: D 19 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.5867 (mm-40) REVERT: D 102 LEU cc_start: 0.7670 (OUTLIER) cc_final: 0.7338 (tt) REVERT: D 156 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8290 (mtp85) REVERT: D 399 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.8072 (mt-10) REVERT: D 438 ASP cc_start: 0.6215 (m-30) cc_final: 0.5754 (t0) outliers start: 67 outliers final: 43 residues processed: 259 average time/residue: 1.3030 time to fit residues: 372.7974 Evaluate side-chains 265 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 208 time to evaluate : 1.556 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain A residue 220 ASN 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 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 102 LEU Chi-restraints excluded: chain B residue 114 LEU 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 320 VAL 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 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 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 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 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 262 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 357 LEU 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 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: 3.9990 chunk 138 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 76 optimal weight: 0.9980 chunk 121 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 186 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 69 GLN B 350 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.157364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137641 restraints weight = 17916.392| |-----------------------------------------------------------------------------| r_work (start): 0.3762 rms_B_bonded: 1.99 r_work: 0.3678 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.2202 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= 0.129 Angle : 0.506 6.520 21352 Z= 0.273 Chirality : 0.042 0.164 2364 Planarity : 0.004 0.038 2736 Dihedral : 7.409 59.605 2338 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 3.68 % Allowed : 19.13 % Favored : 77.19 % 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: 0.59 (0.20), residues: 1964 helix: 1.44 (0.18), residues: 856 sheet: -0.07 (0.26), residues: 420 loop : -0.53 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 453 HIS 0.013 0.002 HIS C 484 PHE 0.012 0.001 PHE B 411 TYR 0.019 0.001 TYR B 351 ARG 0.005 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 797) hydrogen bonds : angle 4.75501 ( 2283) covalent geometry : bond 0.00303 (15748) covalent geometry : angle 0.50630 (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 274 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 214 time to evaluate : 1.816 Fit side-chains REVERT: A 19 GLN cc_start: 0.7121 (OUTLIER) cc_final: 0.5815 (mm-40) REVERT: A 156 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8277 (mtp85) REVERT: A 321 ARG cc_start: 0.6780 (mtm-85) cc_final: 0.6109 (mtp-110) REVERT: A 325 GLU cc_start: 0.6867 (tt0) cc_final: 0.6343 (pt0) REVERT: A 349 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6327 (mp0) REVERT: A 399 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: A 409 MET cc_start: 0.8247 (mtp) cc_final: 0.7657 (mtm) REVERT: B 19 GLN cc_start: 0.6973 (OUTLIER) cc_final: 0.5727 (mm-40) REVERT: B 102 LEU cc_start: 0.7618 (OUTLIER) cc_final: 0.7275 (tt) REVERT: B 262 ASN cc_start: 0.7943 (t0) cc_final: 0.7708 (t0) REVERT: B 321 ARG cc_start: 0.6724 (mtm-85) cc_final: 0.6062 (mtp-110) REVERT: B 325 GLU cc_start: 0.7001 (tt0) cc_final: 0.6430 (pt0) REVERT: B 330 TYR cc_start: 0.7176 (OUTLIER) cc_final: 0.5600 (t80) REVERT: B 341 THR cc_start: 0.7614 (p) cc_final: 0.6402 (p) REVERT: B 363 LYS cc_start: 0.7391 (mtpp) cc_final: 0.6731 (mmtm) REVERT: C 19 GLN cc_start: 0.7109 (OUTLIER) cc_final: 0.5887 (mm-40) REVERT: C 102 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7260 (tt) REVERT: C 156 ARG cc_start: 0.8879 (OUTLIER) cc_final: 0.8295 (mtp85) REVERT: C 262 ASN cc_start: 0.8422 (t0) cc_final: 0.8209 (t0) REVERT: C 321 ARG cc_start: 0.6731 (mtm-85) cc_final: 0.6106 (mtp-110) REVERT: C 325 GLU cc_start: 0.6712 (tt0) cc_final: 0.6247 (pt0) REVERT: C 399 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8100 (mt-10) REVERT: C 409 MET cc_start: 0.8318 (mtp) cc_final: 0.7683 (mtm) REVERT: C 438 ASP cc_start: 0.6336 (m-30) cc_final: 0.5813 (t0) REVERT: D 19 GLN cc_start: 0.7125 (OUTLIER) cc_final: 0.5854 (mm-40) REVERT: D 102 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7290 (tt) REVERT: D 156 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8305 (mtp85) REVERT: D 349 GLU cc_start: 0.6852 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: D 399 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.8094 (mt-10) REVERT: D 409 MET cc_start: 0.8223 (mtp) cc_final: 0.7590 (mtm) REVERT: D 438 ASP cc_start: 0.6158 (m-30) cc_final: 0.5677 (t0) outliers start: 60 outliers final: 40 residues processed: 256 average time/residue: 1.2600 time to fit residues: 358.8213 Evaluate side-chains 267 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 211 time to evaluate : 1.713 ------------------------------------------------------------------------------- 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 209 ILE Chi-restraints excluded: chain A residue 245 THR 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 102 LEU 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 303 CYS Chi-restraints excluded: chain B residue 320 VAL 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 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 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 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 262 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 35 optimal weight: 0.9990 chunk 185 optimal weight: 0.9990 chunk 124 optimal weight: 4.9990 chunk 147 optimal weight: 5.9990 chunk 73 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 99 optimal weight: 4.9990 chunk 176 optimal weight: 0.0770 chunk 45 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9744 ------------------------------------------------------------------------------- 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 = 0.3902 r_free = 0.3902 target = 0.157002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.137425 restraints weight = 17836.731| |-----------------------------------------------------------------------------| r_work (start): 0.3757 rms_B_bonded: 1.98 r_work: 0.3673 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2218 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= 0.140 Angle : 0.516 6.396 21352 Z= 0.278 Chirality : 0.042 0.165 2364 Planarity : 0.004 0.038 2736 Dihedral : 7.364 58.765 2338 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.17 % Allowed : 18.88 % Favored : 76.95 % 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: 1.43 (0.18), residues: 856 sheet: -0.06 (0.26), residues: 420 loop : -0.52 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 178 HIS 0.015 0.002 HIS C 484 PHE 0.012 0.001 PHE B 411 TYR 0.019 0.002 TYR B 351 ARG 0.006 0.000 ARG D 321 Details of bonding type rmsd hydrogen bonds : bond 0.03863 ( 797) hydrogen bonds : angle 4.74930 ( 2283) covalent geometry : bond 0.00333 (15748) covalent geometry : angle 0.51562 (21352) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12878.37 seconds wall clock time: 229 minutes 9.12 seconds (13749.12 seconds total)