Starting phenix.real_space_refine on Fri Jul 3 18:39:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_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_28271/07_2026/8ene_28271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ene_28271/07_2026/8ene_28271.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.043 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 3.67, per 1000 atoms: 0.24 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: 1.24 Conformation dependent library (CDL) restraints added in 662.8 milliseconds 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: 0.51 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: 2.69 Time building geometry restraints manager: 1.67 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: 8218 11.87 - 23.74: 774 23.74 - 35.61: 200 35.61 - 47.48: 67 47.48 - 59.35: 49 Dihedral angle restraints: 9308 sinusoidal: 3708 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 9305 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 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 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 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: 1.960 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: 0.240 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 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 : 11.369 59.347 5740 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.004 0.000 ARG D 131 TYR 0.016 0.001 TYR D 351 PHE 0.009 0.001 PHE D 290 TRP 0.007 0.001 TRP B 453 HIS 0.002 0.001 HIS D 204 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.23 (15748) covalent geometry : angle 0.59751 / 0.31 (21352) hydrogen bonds : bond 0.14039 / 9.73 ( 797) hydrogen bonds : angle 6.65277 / 4.87 ( 2283) *********************** 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 : 0.544 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: 0.4900 (OUTLIER) cc_final: 0.4532 (pp) REVERT: B 341 THR cc_start: 0.7504 (p) cc_final: 0.7218 (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: 0.5679 time to fit residues: 231.8976 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 : 0.426 ------------------------------------------------------------------------------- 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 98 optimal weight: 6.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 299 GLN A 389 ASN A 474 ASN B 157 HIS B 220 ASN B 262 ASN B 299 GLN B 301 GLN B 342 GLN B 389 ASN B 474 ASN C 262 ASN C 299 GLN C 301 GLN C 342 GLN C 389 ASN D 299 GLN D 301 GLN D 342 GLN D 389 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.135413 restraints weight = 18048.855| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.06 r_work: 0.3633 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3526 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3526 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.1593 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= 0.216 Angle : 0.603 8.458 21352 Z= 0.323 Chirality : 0.045 0.163 2364 Planarity : 0.005 0.041 2736 Dihedral : 7.588 58.548 2153 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 4.78 % Allowed : 13.30 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.19), residues: 1964 helix: 1.10 (0.18), residues: 864 sheet: -0.02 (0.25), residues: 420 loop : -0.49 (0.25), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 131 TYR 0.022 0.002 TYR D 351 PHE 0.015 0.002 PHE C 24 TRP 0.012 0.002 TRP D 178 HIS 0.007 0.002 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.22 (15748) covalent geometry : angle 0.60275 / 0.32 (21352) hydrogen bonds : bond 0.05125 / 3.43 ( 797) hydrogen bonds : angle 5.14747 / 3.75 ( 2283) *********************** 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: 78 poor density : 238 time to evaluate : 0.505 Fit side-chains REVERT: A 13 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4975 (pp) REVERT: A 19 GLN cc_start: 0.7010 (OUTLIER) cc_final: 0.5977 (mm-40) REVERT: A 156 ARG cc_start: 0.8920 (OUTLIER) cc_final: 0.8370 (mtp85) REVERT: A 262 ASN cc_start: 0.7424 (OUTLIER) cc_final: 0.7116 (p0) REVERT: A 325 GLU cc_start: 0.6916 (tt0) cc_final: 0.6372 (pt0) REVERT: A 330 TYR cc_start: 0.7201 (OUTLIER) cc_final: 0.5381 (t80) REVERT: A 341 THR cc_start: 0.7451 (p) cc_final: 0.6622 (p) REVERT: A 399 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.8064 (mt-10) REVERT: A 409 MET cc_start: 0.8258 (mtp) cc_final: 0.7594 (mtm) REVERT: B 13 LEU cc_start: 0.5219 (OUTLIER) cc_final: 0.4896 (pp) REVERT: B 19 GLN cc_start: 0.7102 (OUTLIER) cc_final: 0.6169 (mm-40) REVERT: B 325 GLU cc_start: 0.6935 (tt0) cc_final: 0.6420 (pt0) REVERT: B 330 TYR cc_start: 0.7191 (OUTLIER) cc_final: 0.6152 (t80) REVERT: B 341 THR cc_start: 0.7501 (p) cc_final: 0.6855 (p) REVERT: B 416 ASP cc_start: 0.5643 (t70) cc_final: 0.5375 (m-30) REVERT: C 13 LEU cc_start: 0.5127 (OUTLIER) cc_final: 0.4821 (pp) REVERT: C 19 GLN cc_start: 0.7066 (OUTLIER) cc_final: 0.5766 (mm-40) REVERT: C 58 GLU cc_start: 0.7006 (mp0) cc_final: 0.6768 (pm20) REVERT: C 156 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8404 (mtp85) REVERT: C 322 ARG cc_start: 0.7554 (ttm170) cc_final: 0.7247 (mtt-85) REVERT: C 325 GLU cc_start: 0.6700 (tt0) cc_final: 0.6295 (pt0) REVERT: C 329 LYS cc_start: 0.7569 (mtpt) cc_final: 0.7360 (mtpt) REVERT: C 409 MET cc_start: 0.8216 (mtp) cc_final: 0.7546 (mtm) REVERT: D 19 GLN cc_start: 0.7117 (OUTLIER) cc_final: 0.6250 (mm-40) REVERT: D 102 LEU cc_start: 0.7582 (OUTLIER) cc_final: 0.7272 (tt) REVERT: D 156 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8398 (mtp85) REVERT: D 321 ARG cc_start: 0.7321 (mpt180) cc_final: 0.6986 (mpt90) REVERT: D 409 MET cc_start: 0.8237 (mtp) cc_final: 0.7625 (mtm) REVERT: D 438 ASP cc_start: 0.6567 (m-30) cc_final: 0.5864 (t0) REVERT: D 481 TYR cc_start: 0.6990 (t80) cc_final: 0.6449 (t80) REVERT: D 485 GLU cc_start: 0.7902 (OUTLIER) cc_final: 0.6626 (mp0) outliers start: 78 outliers final: 35 residues processed: 275 average time/residue: 0.5708 time to fit residues: 173.9691 Evaluate side-chains 281 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 230 time to evaluate : 0.624 ------------------------------------------------------------------------------- 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 330 TYR 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 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 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 402 PHE Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 437 ILE 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 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 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 D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 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 119 optimal weight: 0.9980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 2.9990 chunk 172 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 98 optimal weight: 5.9990 chunk 31 optimal weight: 0.9980 chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B 350 GLN C 262 ASN C 301 GLN C 350 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.155975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.135853 restraints weight = 18074.915| |-----------------------------------------------------------------------------| r_work (start): 0.3722 rms_B_bonded: 2.06 r_work: 0.3637 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7649 moved from start: 0.1750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 15748 Z= 0.176 Angle : 0.551 6.922 21352 Z= 0.294 Chirality : 0.043 0.161 2364 Planarity : 0.005 0.041 2736 Dihedral : 6.840 58.380 2144 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.41 % Allowed : 16.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1964 helix: 1.28 (0.18), residues: 864 sheet: -0.05 (0.26), residues: 420 loop : -0.53 (0.24), residues: 680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 131 TYR 0.022 0.002 TYR B 351 PHE 0.013 0.001 PHE D 290 TRP 0.013 0.001 TRP D 178 HIS 0.007 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.18 (15748) covalent geometry : angle 0.55104 / 0.29 (21352) hydrogen bonds : bond 0.04573 / 3.07 ( 797) hydrogen bonds : angle 4.93825 / 3.60 ( 2283) *********************** 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 311 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 239 time to evaluate : 0.586 Fit side-chains REVERT: A 19 GLN cc_start: 0.6954 (OUTLIER) cc_final: 0.5930 (mm-40) REVERT: A 156 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8340 (mtp85) REVERT: A 321 ARG cc_start: 0.6832 (mtm-85) cc_final: 0.6170 (mtp-110) REVERT: A 325 GLU cc_start: 0.6837 (tt0) cc_final: 0.6369 (pt0) REVERT: A 330 TYR cc_start: 0.7100 (OUTLIER) cc_final: 0.5382 (t80) REVERT: A 341 THR cc_start: 0.7609 (p) cc_final: 0.6857 (p) REVERT: A 399 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 409 MET cc_start: 0.8255 (mtp) cc_final: 0.7630 (mtm) REVERT: B 19 GLN cc_start: 0.7018 (OUTLIER) cc_final: 0.6090 (mm-40) REVERT: B 121 ASN cc_start: 0.7775 (m110) cc_final: 0.7372 (m-40) REVERT: B 321 ARG cc_start: 0.6808 (mtm-85) cc_final: 0.6149 (mtp-110) REVERT: B 325 GLU cc_start: 0.6950 (tt0) cc_final: 0.6372 (pt0) REVERT: B 330 TYR cc_start: 0.7221 (OUTLIER) cc_final: 0.6007 (t80) REVERT: B 341 THR cc_start: 0.7634 (p) cc_final: 0.6922 (p) REVERT: B 416 ASP cc_start: 0.5645 (t70) cc_final: 0.5356 (m-30) REVERT: C 19 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.5798 (mm-40) REVERT: C 156 ARG cc_start: 0.8932 (OUTLIER) cc_final: 0.8384 (mtp85) REVERT: C 321 ARG cc_start: 0.6768 (mtm-85) cc_final: 0.6145 (mtp-110) REVERT: C 322 ARG cc_start: 0.7591 (ttm170) cc_final: 0.7336 (mtt-85) REVERT: C 325 GLU cc_start: 0.6720 (tt0) cc_final: 0.6262 (pt0) REVERT: C 329 LYS cc_start: 0.7586 (mtpt) cc_final: 0.7326 (mtpt) REVERT: C 399 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.8075 (mt-10) REVERT: C 409 MET cc_start: 0.8241 (mtp) cc_final: 0.7571 (mtm) REVERT: C 485 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.6717 (mp0) REVERT: D 19 GLN cc_start: 0.7068 (OUTLIER) cc_final: 0.6031 (mm-40) REVERT: D 87 ARG cc_start: 0.7986 (tpt90) cc_final: 0.7650 (mmm160) REVERT: D 102 LEU cc_start: 0.7596 (OUTLIER) cc_final: 0.7269 (tt) REVERT: D 156 ARG cc_start: 0.8960 (OUTLIER) cc_final: 0.8409 (mtp85) REVERT: D 409 MET cc_start: 0.8229 (mtp) cc_final: 0.7590 (mtm) REVERT: D 441 ILE cc_start: 0.7187 (mm) cc_final: 0.6978 (mm) REVERT: D 481 TYR cc_start: 0.6950 (t80) cc_final: 0.6414 (t80) REVERT: D 485 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.6564 (mp0) outliers start: 72 outliers final: 40 residues processed: 283 average time/residue: 0.5236 time to fit residues: 164.3515 Evaluate side-chains 280 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 226 time to evaluate : 0.578 ------------------------------------------------------------------------------- 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 330 TYR 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 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 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 360 SER Chi-restraints excluded: chain B residue 415 ASP Chi-restraints excluded: chain B residue 461 SER Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 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 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 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 32 optimal weight: 0.6980 chunk 173 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 188 optimal weight: 0.6980 chunk 160 optimal weight: 0.8980 chunk 70 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 166 optimal weight: 4.9990 chunk 121 optimal weight: 0.8980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN C 262 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3898 r_free = 0.3898 target = 0.156662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136867 restraints weight = 18041.507| |-----------------------------------------------------------------------------| r_work (start): 0.3747 rms_B_bonded: 2.00 r_work: 0.3665 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.1856 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= 0.147 Angle : 0.520 6.165 21352 Z= 0.279 Chirality : 0.042 0.159 2364 Planarity : 0.004 0.041 2736 Dihedral : 6.681 58.376 2144 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.03 % Allowed : 16.37 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.20), residues: 1964 helix: 1.38 (0.18), residues: 860 sheet: -0.07 (0.26), residues: 420 loop : -0.54 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 321 TYR 0.022 0.002 TYR B 351 PHE 0.012 0.001 PHE D 290 TRP 0.008 0.001 TRP D 178 HIS 0.007 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.15 (15748) covalent geometry : angle 0.52020 / 0.28 (21352) hydrogen bonds : bond 0.04182 / 2.79 ( 797) hydrogen bonds : angle 4.84541 / 3.53 ( 2283) *********************** 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 315 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 233 time to evaluate : 0.635 Fit side-chains REVERT: A 19 GLN cc_start: 0.6937 (OUTLIER) cc_final: 0.5864 (mm-40) REVERT: A 156 ARG cc_start: 0.8902 (OUTLIER) cc_final: 0.8356 (mtp85) REVERT: A 321 ARG cc_start: 0.6790 (mtm-85) cc_final: 0.6144 (mtp-110) REVERT: A 325 GLU cc_start: 0.6845 (tt0) cc_final: 0.6368 (pt0) REVERT: A 330 TYR cc_start: 0.7096 (OUTLIER) cc_final: 0.5356 (t80) REVERT: A 341 THR cc_start: 0.7611 (p) cc_final: 0.6858 (p) REVERT: A 399 GLU cc_start: 0.8305 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 409 MET cc_start: 0.8256 (mtp) cc_final: 0.7641 (mtm) REVERT: B 19 GLN cc_start: 0.7049 (OUTLIER) cc_final: 0.6122 (mm-40) REVERT: B 121 ASN cc_start: 0.7797 (m110) cc_final: 0.7425 (m-40) REVERT: B 321 ARG cc_start: 0.6793 (mtm-85) cc_final: 0.6150 (mtp-110) REVERT: B 325 GLU cc_start: 0.6876 (tt0) cc_final: 0.6363 (pt0) REVERT: B 330 TYR cc_start: 0.7112 (OUTLIER) cc_final: 0.5596 (t80) REVERT: B 341 THR cc_start: 0.7639 (p) cc_final: 0.6790 (p) REVERT: B 349 GLU cc_start: 0.6784 (OUTLIER) cc_final: 0.6512 (mp0) REVERT: B 363 LYS cc_start: 0.7363 (mtpp) cc_final: 0.6719 (mmtm) REVERT: B 416 ASP cc_start: 0.5739 (t70) cc_final: 0.5426 (m-30) REVERT: B 485 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7660 (mm-30) REVERT: C 19 GLN cc_start: 0.7054 (OUTLIER) cc_final: 0.5797 (mm-40) REVERT: C 121 ASN cc_start: 0.7663 (m110) cc_final: 0.7389 (m-40) REVERT: C 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8344 (mtp85) REVERT: C 321 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6139 (mtp-110) REVERT: C 325 GLU cc_start: 0.6755 (tt0) cc_final: 0.6307 (pt0) REVERT: C 399 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8083 (mt-10) REVERT: C 409 MET cc_start: 0.8240 (mtp) cc_final: 0.7620 (mtm) REVERT: C 438 ASP cc_start: 0.6435 (m-30) cc_final: 0.5884 (t0) REVERT: D 19 GLN cc_start: 0.7063 (OUTLIER) cc_final: 0.5974 (mm-40) REVERT: D 102 LEU cc_start: 0.7724 (OUTLIER) cc_final: 0.7408 (tt) REVERT: D 156 ARG cc_start: 0.8929 (OUTLIER) cc_final: 0.8353 (mtp85) REVERT: D 349 GLU cc_start: 0.6853 (OUTLIER) cc_final: 0.6407 (mp0) REVERT: D 409 MET cc_start: 0.8239 (mtp) cc_final: 0.7605 (mtm) REVERT: D 438 ASP cc_start: 0.6206 (m-30) cc_final: 0.5728 (t0) REVERT: D 441 ILE cc_start: 0.7172 (mm) cc_final: 0.6961 (mm) outliers start: 82 outliers final: 51 residues processed: 282 average time/residue: 0.5900 time to fit residues: 184.7339 Evaluate side-chains 288 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 222 time to evaluate : 0.628 ------------------------------------------------------------------------------- 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 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR 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 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 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 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 349 GLU 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 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 160 ILE Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE 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 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 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 0 optimal weight: 5.9990 chunk 163 optimal weight: 0.7980 chunk 185 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 158 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN C 262 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.156617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.136680 restraints weight = 17963.706| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.05 r_work: 0.3660 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3558 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.1950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15748 Z= 0.144 Angle : 0.514 5.676 21352 Z= 0.275 Chirality : 0.042 0.164 2364 Planarity : 0.004 0.040 2736 Dihedral : 6.582 58.516 2144 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 5.52 % Allowed : 16.62 % Favored : 77.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.20), residues: 1964 helix: 1.43 (0.18), residues: 860 sheet: -0.09 (0.26), residues: 420 loop : -0.54 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 321 TYR 0.021 0.002 TYR B 351 PHE 0.011 0.001 PHE D 290 TRP 0.007 0.001 TRP D 178 HIS 0.007 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 (15748) covalent geometry : angle 0.51382 / 0.28 (21352) hydrogen bonds : bond 0.04041 / 2.70 ( 797) hydrogen bonds : angle 4.79143 / 3.49 ( 2283) *********************** 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 316 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 226 time to evaluate : 0.646 Fit side-chains REVERT: A 19 GLN cc_start: 0.6972 (OUTLIER) cc_final: 0.5927 (mm-40) REVERT: A 109 MET cc_start: 0.7387 (OUTLIER) cc_final: 0.7103 (ttp) REVERT: A 156 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8350 (mtp85) REVERT: A 321 ARG cc_start: 0.6785 (mtm-85) cc_final: 0.6140 (mtp-110) REVERT: A 325 GLU cc_start: 0.6894 (tt0) cc_final: 0.6358 (pt0) REVERT: A 330 TYR cc_start: 0.7059 (OUTLIER) cc_final: 0.5331 (t80) REVERT: A 341 THR cc_start: 0.7413 (p) cc_final: 0.6615 (p) REVERT: A 349 GLU cc_start: 0.6829 (OUTLIER) cc_final: 0.6546 (mp0) REVERT: A 399 GLU cc_start: 0.8304 (OUTLIER) cc_final: 0.8045 (mt-10) REVERT: A 409 MET cc_start: 0.8254 (mtp) cc_final: 0.7638 (mtm) REVERT: B 19 GLN cc_start: 0.7031 (OUTLIER) cc_final: 0.6058 (mm-40) REVERT: B 109 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7092 (ttp) REVERT: B 121 ASN cc_start: 0.7858 (m110) cc_final: 0.7439 (m-40) REVERT: B 321 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.6130 (mtp-110) REVERT: B 325 GLU cc_start: 0.6856 (tt0) cc_final: 0.6348 (pt0) REVERT: B 330 TYR cc_start: 0.7098 (OUTLIER) cc_final: 0.5609 (t80) REVERT: B 341 THR cc_start: 0.7634 (p) cc_final: 0.6724 (p) REVERT: B 349 GLU cc_start: 0.6837 (OUTLIER) cc_final: 0.6571 (mp0) REVERT: B 416 ASP cc_start: 0.5751 (t70) cc_final: 0.5416 (m-30) REVERT: B 485 GLU cc_start: 0.7860 (OUTLIER) cc_final: 0.7600 (mm-30) REVERT: C 19 GLN cc_start: 0.7036 (OUTLIER) cc_final: 0.5792 (mm-40) REVERT: C 121 ASN cc_start: 0.7670 (m110) cc_final: 0.7421 (m-40) REVERT: C 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8333 (mtp85) REVERT: C 321 ARG cc_start: 0.6729 (mtm-85) cc_final: 0.6121 (mtp-110) REVERT: C 325 GLU cc_start: 0.6714 (tt0) cc_final: 0.6266 (pt0) REVERT: C 399 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: C 409 MET cc_start: 0.8330 (mtp) cc_final: 0.7707 (mtm) REVERT: C 438 ASP cc_start: 0.6419 (m-30) cc_final: 0.5873 (t0) REVERT: D 19 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.5986 (mm-40) REVERT: D 102 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7366 (tt) REVERT: D 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8330 (mtp85) REVERT: D 321 ARG cc_start: 0.7141 (mpt180) cc_final: 0.6741 (mpt90) REVERT: D 349 GLU cc_start: 0.6865 (OUTLIER) cc_final: 0.6408 (mp0) REVERT: D 438 ASP cc_start: 0.6182 (m-30) cc_final: 0.5700 (t0) outliers start: 90 outliers final: 52 residues processed: 283 average time/residue: 0.5681 time to fit residues: 179.1653 Evaluate side-chains 289 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 219 time to evaluate : 0.603 ------------------------------------------------------------------------------- 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 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 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 330 TYR 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 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 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 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 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 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 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 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 71 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 167 optimal weight: 0.9980 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 190 optimal weight: 4.9990 chunk 117 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 110 ASN A 350 GLN B 110 ASN B 262 ASN B 301 GLN B 350 GLN C 262 ASN D 110 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.152787 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.133143 restraints weight = 18047.266| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 1.98 r_work: 0.3626 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3524 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7698 moved from start: 0.2091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 15748 Z= 0.272 Angle : 0.632 7.805 21352 Z= 0.335 Chirality : 0.047 0.171 2364 Planarity : 0.005 0.045 2736 Dihedral : 7.027 59.453 2144 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.44 % Allowed : 16.13 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.19), residues: 1964 helix: 1.09 (0.18), residues: 856 sheet: -0.25 (0.26), residues: 408 loop : -0.69 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 131 TYR 0.025 0.002 TYR B 351 PHE 0.016 0.002 PHE C 24 TRP 0.010 0.002 TRP C 453 HIS 0.008 0.002 HIS B 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00673 / 0.27 (15748) covalent geometry : angle 0.63163 / 0.34 (21352) hydrogen bonds : bond 0.05285 / 3.54 ( 797) hydrogen bonds : angle 5.05377 / 3.70 ( 2283) *********************** 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 324 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 219 time to evaluate : 0.649 Fit side-chains REVERT: A 19 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.5897 (mm-40) REVERT: A 109 MET cc_start: 0.7488 (OUTLIER) cc_final: 0.7185 (ttp) REVERT: A 321 ARG cc_start: 0.6875 (mtm-85) cc_final: 0.6179 (mtp-110) REVERT: A 325 GLU cc_start: 0.6966 (tt0) cc_final: 0.6441 (pt0) REVERT: A 330 TYR cc_start: 0.7062 (OUTLIER) cc_final: 0.4895 (t80) REVERT: A 341 THR cc_start: 0.7509 (p) cc_final: 0.6905 (p) REVERT: A 349 GLU cc_start: 0.6807 (OUTLIER) cc_final: 0.6499 (mp0) REVERT: A 399 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: B 19 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.6041 (mm-40) REVERT: B 109 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.7080 (ttp) REVERT: B 121 ASN cc_start: 0.7726 (m110) cc_final: 0.7276 (m-40) REVERT: B 321 ARG cc_start: 0.6844 (mtm-85) cc_final: 0.6155 (mtp-110) REVERT: B 325 GLU cc_start: 0.6988 (tt0) cc_final: 0.6505 (pt0) REVERT: B 330 TYR cc_start: 0.7203 (OUTLIER) cc_final: 0.5457 (t80) REVERT: B 341 THR cc_start: 0.7680 (p) cc_final: 0.6634 (p) REVERT: B 349 GLU cc_start: 0.6833 (OUTLIER) cc_final: 0.6537 (mp0) REVERT: B 485 GLU cc_start: 0.7945 (OUTLIER) cc_final: 0.7689 (mm-30) REVERT: C 19 GLN cc_start: 0.7107 (OUTLIER) cc_final: 0.5886 (mm-40) REVERT: C 102 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7355 (tt) REVERT: C 156 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8389 (mtp85) REVERT: C 321 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.6138 (mtp-110) REVERT: C 325 GLU cc_start: 0.6720 (tt0) cc_final: 0.6257 (pt0) REVERT: C 349 GLU cc_start: 0.6904 (OUTLIER) cc_final: 0.6396 (mp0) REVERT: C 399 GLU cc_start: 0.8281 (OUTLIER) cc_final: 0.8036 (mt-10) REVERT: C 409 MET cc_start: 0.8370 (mtp) cc_final: 0.7698 (mtm) REVERT: C 485 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.6652 (mp0) REVERT: D 19 GLN cc_start: 0.7196 (OUTLIER) cc_final: 0.5998 (mm-40) REVERT: D 102 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7298 (tt) REVERT: D 156 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8392 (mtp85) REVERT: D 349 GLU cc_start: 0.6902 (OUTLIER) cc_final: 0.6622 (mp0) REVERT: D 399 GLU cc_start: 0.8367 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: D 485 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.6575 (mp0) outliers start: 105 outliers final: 54 residues processed: 291 average time/residue: 0.5708 time to fit residues: 185.2307 Evaluate side-chains 290 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 214 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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 160 ILE 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 320 VAL Chi-restraints excluded: chain A residue 330 TYR 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 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 109 MET 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 320 VAL 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 102 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 220 ASN 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 349 GLU 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 417 VAL 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 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU 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 485 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 151 optimal weight: 3.9990 chunk 183 optimal weight: 0.0970 chunk 168 optimal weight: 0.5980 chunk 37 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 154 optimal weight: 0.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 301 GLN C 262 ASN C 301 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3911 r_free = 0.3911 target = 0.157723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.138103 restraints weight = 17804.276| |-----------------------------------------------------------------------------| r_work (start): 0.3756 rms_B_bonded: 1.98 r_work: 0.3675 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3572 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.2114 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= 0.116 Angle : 0.495 6.360 21352 Z= 0.267 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.040 2736 Dihedral : 6.315 59.745 2140 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.41 % Allowed : 18.76 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.19), residues: 1964 helix: 1.39 (0.18), residues: 856 sheet: -0.10 (0.26), residues: 420 loop : -0.57 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 321 TYR 0.020 0.001 TYR B 351 PHE 0.010 0.001 PHE C 290 TRP 0.015 0.001 TRP A 453 HIS 0.008 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 (15748) covalent geometry : angle 0.49477 / 0.27 (21352) hydrogen bonds : bond 0.03640 / 2.43 ( 797) hydrogen bonds : angle 4.75639 / 3.47 ( 2283) *********************** 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 300 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 228 time to evaluate : 0.615 Fit side-chains REVERT: A 19 GLN cc_start: 0.6980 (OUTLIER) cc_final: 0.5771 (mm-40) REVERT: A 156 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8365 (mtp85) REVERT: A 321 ARG cc_start: 0.6743 (mtm-85) cc_final: 0.6102 (mtp-110) REVERT: A 325 GLU cc_start: 0.6870 (tt0) cc_final: 0.6366 (pt0) REVERT: A 330 TYR cc_start: 0.7105 (OUTLIER) cc_final: 0.5122 (t80) REVERT: A 341 THR cc_start: 0.7366 (p) cc_final: 0.6773 (p) REVERT: B 19 GLN cc_start: 0.7004 (OUTLIER) cc_final: 0.5842 (mm-40) REVERT: B 121 ASN cc_start: 0.7814 (m110) cc_final: 0.7412 (m-40) REVERT: B 321 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6055 (mtp-110) REVERT: B 325 GLU cc_start: 0.6962 (tt0) cc_final: 0.6439 (pt0) REVERT: B 330 TYR cc_start: 0.7106 (OUTLIER) cc_final: 0.5580 (t80) REVERT: B 341 THR cc_start: 0.7680 (p) cc_final: 0.6644 (p) REVERT: B 363 LYS cc_start: 0.7381 (mtpp) cc_final: 0.6730 (mmtm) REVERT: B 389 ASN cc_start: 0.7726 (m-40) cc_final: 0.7473 (m-40) REVERT: B 416 ASP cc_start: 0.5762 (t70) cc_final: 0.5443 (m-30) REVERT: C 19 GLN cc_start: 0.7129 (OUTLIER) cc_final: 0.5878 (mm-40) REVERT: C 102 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7213 (tt) REVERT: C 156 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8298 (mtp85) REVERT: C 321 ARG cc_start: 0.6695 (mtm-85) cc_final: 0.6080 (mtp-110) REVERT: C 325 GLU cc_start: 0.6685 (tt0) cc_final: 0.6225 (pt0) REVERT: C 399 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: C 409 MET cc_start: 0.8316 (mtp) cc_final: 0.7673 (mtm) REVERT: C 438 ASP cc_start: 0.6244 (m-30) cc_final: 0.5745 (t0) REVERT: D 19 GLN cc_start: 0.7139 (OUTLIER) cc_final: 0.5911 (mm-40) REVERT: D 102 LEU cc_start: 0.7645 (OUTLIER) cc_final: 0.7279 (tt) REVERT: D 156 ARG cc_start: 0.8894 (OUTLIER) cc_final: 0.8272 (mtp85) REVERT: D 409 MET cc_start: 0.8104 (mtp) cc_final: 0.7643 (mtm) REVERT: D 438 ASP cc_start: 0.6174 (m-30) cc_final: 0.5674 (t0) outliers start: 72 outliers final: 42 residues processed: 271 average time/residue: 0.5612 time to fit residues: 169.9402 Evaluate side-chains 276 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 222 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 330 TYR Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR 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 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 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 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 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 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 412 LYS 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 39 optimal weight: 4.9990 chunk 150 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 152 optimal weight: 3.9990 chunk 149 optimal weight: 0.9990 chunk 99 optimal weight: 4.9990 chunk 184 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 262 ASN B 301 GLN C 262 ASN C 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.155328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.135642 restraints weight = 18010.547| |-----------------------------------------------------------------------------| r_work (start): 0.3736 rms_B_bonded: 1.99 r_work: 0.3654 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3553 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 15748 Z= 0.189 Angle : 0.551 7.338 21352 Z= 0.295 Chirality : 0.044 0.167 2364 Planarity : 0.005 0.038 2736 Dihedral : 6.451 58.954 2140 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 5.09 % Allowed : 18.52 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.42 (0.19), residues: 1964 helix: 1.29 (0.18), residues: 856 sheet: -0.17 (0.25), residues: 420 loop : -0.61 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 321 TYR 0.022 0.002 TYR B 351 PHE 0.013 0.002 PHE D 411 TRP 0.006 0.002 TRP D 29 HIS 0.009 0.001 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.19 (15748) covalent geometry : angle 0.55117 / 0.29 (21352) hydrogen bonds : bond 0.04365 / 2.92 ( 797) hydrogen bonds : angle 4.84794 / 3.54 ( 2283) *********************** 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 300 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 217 time to evaluate : 0.612 Fit side-chains REVERT: A 19 GLN cc_start: 0.7024 (OUTLIER) cc_final: 0.5797 (mm-40) REVERT: A 156 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8360 (mtp85) REVERT: A 321 ARG cc_start: 0.6799 (mtm-85) cc_final: 0.6126 (mtp-110) REVERT: A 325 GLU cc_start: 0.6910 (tt0) cc_final: 0.6396 (pt0) REVERT: A 330 TYR cc_start: 0.7131 (OUTLIER) cc_final: 0.5025 (t80) REVERT: A 341 THR cc_start: 0.7454 (p) cc_final: 0.6818 (p) REVERT: A 349 GLU cc_start: 0.6841 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: A 399 GLU cc_start: 0.8265 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: B 19 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.5994 (mm-40) REVERT: B 102 LEU cc_start: 0.7623 (OUTLIER) cc_final: 0.7297 (tt) REVERT: B 121 ASN cc_start: 0.7627 (m110) cc_final: 0.7185 (m-40) REVERT: B 175 MET cc_start: 0.8089 (mmt) cc_final: 0.7882 (mmt) REVERT: B 321 ARG cc_start: 0.6781 (mtm-85) cc_final: 0.6104 (mtp-110) REVERT: B 325 GLU cc_start: 0.7018 (tt0) cc_final: 0.6479 (pt0) REVERT: B 330 TYR cc_start: 0.7196 (OUTLIER) cc_final: 0.5403 (t80) REVERT: B 341 THR cc_start: 0.7645 (p) cc_final: 0.6461 (p) REVERT: B 485 GLU cc_start: 0.7889 (OUTLIER) cc_final: 0.7675 (mm-30) REVERT: C 19 GLN cc_start: 0.7120 (OUTLIER) cc_final: 0.5871 (mm-40) REVERT: C 102 LEU cc_start: 0.7592 (OUTLIER) cc_final: 0.7260 (tt) REVERT: C 156 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8329 (mtp85) REVERT: C 321 ARG cc_start: 0.6741 (mtm-85) cc_final: 0.6092 (mtp-110) REVERT: C 325 GLU cc_start: 0.6693 (tt0) cc_final: 0.6236 (pt0) REVERT: C 399 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.8061 (mt-10) REVERT: C 409 MET cc_start: 0.8366 (mtp) cc_final: 0.7695 (mtm) REVERT: C 485 GLU cc_start: 0.7901 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: D 19 GLN cc_start: 0.7143 (OUTLIER) cc_final: 0.5851 (mm-40) REVERT: D 102 LEU cc_start: 0.7659 (OUTLIER) cc_final: 0.7323 (tt) REVERT: D 156 ARG cc_start: 0.8921 (OUTLIER) cc_final: 0.8324 (mtp85) REVERT: D 349 GLU cc_start: 0.6873 (OUTLIER) cc_final: 0.6355 (mp0) REVERT: D 399 GLU cc_start: 0.8349 (OUTLIER) cc_final: 0.8103 (mt-10) REVERT: D 438 ASP cc_start: 0.6199 (m-30) cc_final: 0.5715 (t0) outliers start: 83 outliers final: 44 residues processed: 274 average time/residue: 0.5432 time to fit residues: 165.2881 Evaluate side-chains 278 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 215 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 320 VAL Chi-restraints excluded: chain A residue 330 TYR 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 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL Chi-restraints excluded: chain B residue 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 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 209 ILE Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 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 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 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 168 optimal weight: 0.5980 chunk 195 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 190 optimal weight: 4.9990 chunk 172 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN B 301 GLN C 69 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3893 r_free = 0.3893 target = 0.155876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.136287 restraints weight = 17890.766| |-----------------------------------------------------------------------------| r_work (start): 0.3746 rms_B_bonded: 1.98 r_work: 0.3663 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3562 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7655 moved from start: 0.2166 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= 0.164 Angle : 0.537 6.716 21352 Z= 0.288 Chirality : 0.043 0.165 2364 Planarity : 0.004 0.039 2736 Dihedral : 6.443 59.284 2140 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.90 % Allowed : 18.76 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1964 helix: 1.28 (0.18), residues: 860 sheet: -0.14 (0.26), residues: 420 loop : -0.59 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 321 TYR 0.021 0.002 TYR B 351 PHE 0.012 0.001 PHE D 411 TRP 0.006 0.001 TRP A 29 HIS 0.010 0.001 HIS D 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00397 / 0.16 (15748) covalent geometry : angle 0.53666 / 0.29 (21352) hydrogen bonds : bond 0.04171 / 2.79 ( 797) hydrogen bonds : angle 4.81665 / 3.52 ( 2283) *********************** 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 295 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 215 time to evaluate : 0.632 Fit side-chains REVERT: A 19 GLN cc_start: 0.7057 (OUTLIER) cc_final: 0.5823 (mm-40) REVERT: A 156 ARG cc_start: 0.8898 (OUTLIER) cc_final: 0.8320 (mtp85) REVERT: A 321 ARG cc_start: 0.6785 (mtm-85) cc_final: 0.6116 (mtp-110) REVERT: A 325 GLU cc_start: 0.6997 (tt0) cc_final: 0.6486 (pt0) REVERT: A 330 TYR cc_start: 0.7085 (OUTLIER) cc_final: 0.4885 (t80) REVERT: A 341 THR cc_start: 0.7474 (p) cc_final: 0.6824 (p) REVERT: A 399 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 19 GLN cc_start: 0.7059 (OUTLIER) cc_final: 0.5840 (mm-40) REVERT: B 102 LEU cc_start: 0.7611 (OUTLIER) cc_final: 0.7275 (tt) REVERT: B 121 ASN cc_start: 0.7719 (m110) cc_final: 0.7268 (m-40) REVERT: B 321 ARG cc_start: 0.6759 (mtm-85) cc_final: 0.6086 (mtp-110) REVERT: B 325 GLU cc_start: 0.7046 (tt0) cc_final: 0.6487 (pt0) REVERT: B 330 TYR cc_start: 0.7240 (OUTLIER) cc_final: 0.5638 (t80) REVERT: B 341 THR cc_start: 0.7648 (p) cc_final: 0.6371 (p) REVERT: B 363 LYS cc_start: 0.7481 (mtpp) cc_final: 0.6827 (mmtm) REVERT: B 485 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7691 (mm-30) REVERT: C 19 GLN cc_start: 0.7114 (OUTLIER) cc_final: 0.5873 (mm-40) REVERT: C 102 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7270 (tt) REVERT: C 156 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8328 (mtp85) REVERT: C 321 ARG cc_start: 0.6746 (mtm-85) cc_final: 0.6085 (mtp-110) REVERT: C 325 GLU cc_start: 0.6678 (tt0) cc_final: 0.6220 (pt0) REVERT: C 399 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8068 (mt-10) REVERT: C 409 MET cc_start: 0.8349 (mtp) cc_final: 0.7682 (mtm) REVERT: D 19 GLN cc_start: 0.7163 (OUTLIER) cc_final: 0.5892 (mm-40) REVERT: D 102 LEU cc_start: 0.7650 (OUTLIER) cc_final: 0.7308 (tt) REVERT: D 156 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8327 (mtp85) REVERT: D 399 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.8116 (mt-10) REVERT: D 438 ASP cc_start: 0.6198 (m-30) cc_final: 0.5714 (t0) outliers start: 80 outliers final: 42 residues processed: 270 average time/residue: 0.5982 time to fit residues: 179.3110 Evaluate side-chains 266 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 208 time to evaluate : 0.631 ------------------------------------------------------------------------------- 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 156 ARG 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 330 TYR 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 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 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 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 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 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 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 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 184 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 2.9990 chunk 165 optimal weight: 0.7980 chunk 117 optimal weight: 0.8980 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 0.6980 chunk 41 optimal weight: 6.9990 chunk 103 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN B 301 GLN C 69 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.156272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.136640 restraints weight = 17948.857| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.99 r_work: 0.3666 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3565 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15748 Z= 0.147 Angle : 0.531 6.467 21352 Z= 0.285 Chirality : 0.042 0.164 2364 Planarity : 0.004 0.038 2736 Dihedral : 6.367 59.344 2140 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 4.41 % Allowed : 19.44 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.19), residues: 1964 helix: 1.33 (0.18), residues: 860 sheet: -0.09 (0.26), residues: 420 loop : -0.57 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 321 TYR 0.020 0.002 TYR B 351 PHE 0.012 0.001 PHE D 411 TRP 0.006 0.001 TRP C 178 HIS 0.013 0.002 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (15748) covalent geometry : angle 0.53111 / 0.28 (21352) hydrogen bonds : bond 0.04000 / 2.67 ( 797) hydrogen bonds : angle 4.78419 / 3.50 ( 2283) ********************** 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 286 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 214 time to evaluate : 0.597 Fit side-chains REVERT: A 19 GLN cc_start: 0.7046 (OUTLIER) cc_final: 0.5764 (mm-40) REVERT: A 156 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8347 (mtp85) REVERT: A 321 ARG cc_start: 0.6767 (mtm-85) cc_final: 0.6098 (mtp-110) REVERT: A 325 GLU cc_start: 0.6978 (tt0) cc_final: 0.6454 (pt0) REVERT: A 330 TYR cc_start: 0.7053 (OUTLIER) cc_final: 0.4959 (t80) REVERT: A 341 THR cc_start: 0.7419 (p) cc_final: 0.6808 (p) REVERT: A 349 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: A 399 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.8001 (mt-10) REVERT: B 19 GLN cc_start: 0.7040 (OUTLIER) cc_final: 0.5816 (mm-40) REVERT: B 102 LEU cc_start: 0.7655 (OUTLIER) cc_final: 0.7311 (tt) REVERT: B 321 ARG cc_start: 0.6745 (mtm-85) cc_final: 0.6073 (mtp-110) REVERT: B 325 GLU cc_start: 0.7025 (tt0) cc_final: 0.6455 (pt0) REVERT: B 330 TYR cc_start: 0.7177 (OUTLIER) cc_final: 0.5481 (t80) REVERT: B 341 THR cc_start: 0.7624 (p) cc_final: 0.6324 (p) REVERT: B 363 LYS cc_start: 0.7390 (mtpp) cc_final: 0.6731 (mmtm) REVERT: B 416 ASP cc_start: 0.5812 (t70) cc_final: 0.5463 (m-30) REVERT: C 19 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.5855 (mm-40) REVERT: C 102 LEU cc_start: 0.7568 (OUTLIER) cc_final: 0.7234 (tt) REVERT: C 156 ARG cc_start: 0.8915 (OUTLIER) cc_final: 0.8358 (mtp85) REVERT: C 321 ARG cc_start: 0.6733 (mtm-85) cc_final: 0.6073 (mtp-110) REVERT: C 325 GLU cc_start: 0.6668 (tt0) cc_final: 0.6210 (pt0) REVERT: C 399 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: C 409 MET cc_start: 0.8332 (mtp) cc_final: 0.7665 (mtm) REVERT: D 19 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.5885 (mm-40) REVERT: D 102 LEU cc_start: 0.7643 (OUTLIER) cc_final: 0.7295 (tt) REVERT: D 156 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8356 (mtp85) REVERT: D 399 GLU cc_start: 0.8351 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: D 438 ASP cc_start: 0.6184 (m-30) cc_final: 0.5697 (t0) outliers start: 72 outliers final: 45 residues processed: 259 average time/residue: 0.5852 time to fit residues: 168.2522 Evaluate side-chains 269 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 208 time to evaluate : 0.600 ------------------------------------------------------------------------------- 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 167 ILE 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 320 VAL Chi-restraints excluded: chain A residue 330 TYR 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 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 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 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 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 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 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 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 8 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 174 optimal weight: 0.0980 chunk 118 optimal weight: 0.5980 chunk 65 optimal weight: 0.6980 chunk 172 optimal weight: 7.9990 chunk 39 optimal weight: 3.9990 chunk 1 optimal weight: 0.3980 chunk 187 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 179 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 69 GLN B 69 GLN B 301 GLN C 69 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.158536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.138772 restraints weight = 17657.869| |-----------------------------------------------------------------------------| r_work (start): 0.3771 rms_B_bonded: 2.03 r_work: 0.3689 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3586 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7605 moved from start: 0.2222 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= 0.111 Angle : 0.495 6.441 21352 Z= 0.267 Chirality : 0.042 0.161 2364 Planarity : 0.004 0.039 2736 Dihedral : 6.133 58.041 2140 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.43 % Allowed : 20.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.20), residues: 1964 helix: 1.49 (0.18), residues: 860 sheet: 0.18 (0.26), residues: 412 loop : -0.49 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 321 TYR 0.019 0.001 TYR B 351 PHE 0.010 0.001 PHE D 411 TRP 0.009 0.001 TRP A 453 HIS 0.014 0.002 HIS C 484 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (15748) covalent geometry : angle 0.49459 / 0.27 (21352) hydrogen bonds : bond 0.03455 / 2.30 ( 797) hydrogen bonds : angle 4.67776 / 3.41 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5279.89 seconds wall clock time: 90 minutes 57.98 seconds (5457.98 seconds total)