Starting phenix.real_space_refine on Sun Aug 24 00:04:06 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_28271.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_28271.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_28271.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_28271.map" model { file = "/net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_28271.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ene_28271/08_2025/8ene_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-2.0-5787/lib/python3.9/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: 3.32, per 1000 atoms: 0.22 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: 1.17 Conformation dependent library (CDL) restraints added in 639.9 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 0.62 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: 2.81 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5004 1.34 - 1.46: 3410 1.46 - 1.58: 7214 1.58 - 1.69: 12 1.69 - 1.81: 108 Bond restraints: 15748 Sorted by residual: bond pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.98e+01 bond pdb=" C3N NAD A 601 " pdb=" C4N NAD A 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.96e+01 bond pdb=" C3N NAD D 601 " pdb=" C4N NAD D 601 " ideal model delta sigma weight residual 1.390 1.499 -0.109 2.00e-02 2.50e+03 2.95e+01 bond pdb=" C3N NAD B 601 " pdb=" C4N NAD B 601 " ideal model delta sigma weight residual 1.390 1.498 -0.108 2.00e-02 2.50e+03 2.94e+01 bond pdb=" C4N NAD B 601 " pdb=" C5N NAD B 601 " ideal model delta sigma weight residual 1.384 1.485 -0.101 2.00e-02 2.50e+03 2.54e+01 ... (remaining 15743 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.06: 21058 2.06 - 4.11: 254 4.11 - 6.17: 24 6.17 - 8.23: 8 8.23 - 10.28: 8 Bond angle restraints: 21352 Sorted by residual: angle pdb=" PA NAD A 601 " pdb=" O3 NAD A 601 " pdb=" PN NAD A 601 " ideal model delta sigma weight residual 126.50 136.78 -10.28 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD D 601 " pdb=" O3 NAD D 601 " pdb=" PN NAD D 601 " ideal model delta sigma weight residual 126.50 136.74 -10.24 3.00e+00 1.11e-01 1.17e+01 angle pdb=" PA NAD B 601 " pdb=" O3 NAD B 601 " pdb=" PN NAD B 601 " ideal model delta sigma weight residual 126.50 136.70 -10.20 3.00e+00 1.11e-01 1.16e+01 angle pdb=" PA NAD C 601 " pdb=" O3 NAD C 601 " pdb=" PN NAD C 601 " ideal model delta sigma weight residual 126.50 136.68 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C3N NAD C 601 " pdb=" C4N NAD C 601 " pdb=" C5N NAD C 601 " ideal model delta sigma weight residual 119.68 110.28 9.40 3.00e+00 1.11e-01 9.81e+00 ... (remaining 21347 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.87: 8304 11.87 - 23.74: 792 23.74 - 35.61: 231 35.61 - 47.48: 98 47.48 - 59.35: 83 Dihedral angle restraints: 9508 sinusoidal: 3908 harmonic: 5600 Sorted by residual: dihedral pdb=" CA THR D 144 " pdb=" C THR D 144 " pdb=" N ILE D 145 " pdb=" CA ILE D 145 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA THR C 144 " pdb=" C THR C 144 " pdb=" N ILE C 145 " pdb=" CA ILE C 145 " ideal model delta harmonic sigma weight residual -180.00 -160.98 -19.02 0 5.00e+00 4.00e-02 1.45e+01 dihedral pdb=" CA THR A 144 " pdb=" C THR A 144 " pdb=" N ILE A 145 " pdb=" CA ILE A 145 " ideal model delta harmonic sigma weight residual 180.00 -161.82 -18.18 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 9505 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1504 0.031 - 0.061: 550 0.061 - 0.092: 159 0.092 - 0.123: 144 0.123 - 0.154: 7 Chirality restraints: 2364 Sorted by residual: chirality pdb=" C2B NAD D 601 " pdb=" C1B NAD D 601 " pdb=" C3B NAD D 601 " pdb=" O2B NAD D 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.69 0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" C2B NAD B 601 " pdb=" C1B NAD B 601 " pdb=" C3B NAD B 601 " pdb=" O2B NAD B 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.80e-01 chirality pdb=" C2B NAD C 601 " pdb=" C1B NAD C 601 " pdb=" C3B NAD C 601 " pdb=" O2B NAD C 601 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 2361 not shown) Planarity restraints: 2736 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1D NAD B 601 " -0.025 2.00e-02 2.50e+03 6.53e-02 8.52e+01 pdb=" C2N NAD B 601 " -0.057 2.00e-02 2.50e+03 pdb=" C3N NAD B 601 " -0.059 2.00e-02 2.50e+03 pdb=" C4N NAD B 601 " -0.068 2.00e-02 2.50e+03 pdb=" C5N NAD B 601 " -0.010 2.00e-02 2.50e+03 pdb=" C6N NAD B 601 " 0.109 2.00e-02 2.50e+03 pdb=" C7N NAD B 601 " 0.100 2.00e-02 2.50e+03 pdb=" N1N NAD B 601 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD D 601 " 0.024 2.00e-02 2.50e+03 5.70e-02 6.49e+01 pdb=" C2N NAD D 601 " 0.047 2.00e-02 2.50e+03 pdb=" C3N NAD D 601 " 0.054 2.00e-02 2.50e+03 pdb=" C4N NAD D 601 " 0.051 2.00e-02 2.50e+03 pdb=" C5N NAD D 601 " 0.020 2.00e-02 2.50e+03 pdb=" C6N NAD D 601 " -0.101 2.00e-02 2.50e+03 pdb=" C7N NAD D 601 " -0.084 2.00e-02 2.50e+03 pdb=" N1N NAD D 601 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1D NAD A 601 " -0.009 2.00e-02 2.50e+03 4.55e-02 4.14e+01 pdb=" C2N NAD A 601 " 0.056 2.00e-02 2.50e+03 pdb=" C3N NAD A 601 " 0.057 2.00e-02 2.50e+03 pdb=" C4N NAD A 601 " 0.034 2.00e-02 2.50e+03 pdb=" C5N NAD A 601 " -0.009 2.00e-02 2.50e+03 pdb=" C6N NAD A 601 " -0.049 2.00e-02 2.50e+03 pdb=" C7N NAD A 601 " -0.080 2.00e-02 2.50e+03 pdb=" N1N NAD A 601 " -0.000 2.00e-02 2.50e+03 ... (remaining 2733 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 3481 2.79 - 3.32: 14534 3.32 - 3.84: 26298 3.84 - 4.37: 32370 4.37 - 4.90: 54688 Nonbonded interactions: 131371 Sorted by model distance: nonbonded pdb=" O SER B 307 " pdb=" NE2 GLN B 407 " model vdw 2.262 3.120 nonbonded pdb=" OD1 ASP C 281 " pdb=" OG1 THR C 434 " model vdw 2.269 3.040 nonbonded pdb=" OD1 ASP A 281 " pdb=" OG1 THR A 434 " model vdw 2.273 3.040 nonbonded pdb=" OG SER B 461 " pdb=" OE1 GLN B 463 " model vdw 2.274 3.040 nonbonded pdb=" O SER A 307 " pdb=" NE2 GLN A 407 " model vdw 2.290 3.120 ... (remaining 131366 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 9 through 16 or (resid 17 and (name N or name CA or name C \ or name O or name CB )) or resid 18 through 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: 1.680 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: 0.210 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 13.940 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7339 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.109 15748 Z= 0.228 Angle : 0.598 10.283 21352 Z= 0.308 Chirality : 0.041 0.154 2364 Planarity : 0.005 0.065 2736 Dihedral : 12.542 59.347 5940 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.15 % Allowed : 6.01 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.46 (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 covalent geometry : bond 0.00463 (15748) covalent geometry : angle 0.59751 (21352) hydrogen bonds : bond 0.14039 ( 797) hydrogen bonds : angle 6.65277 ( 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 : 0.579 Fit side-chains revert: symmetry clash REVERT: A 13 LEU cc_start: 0.5007 (OUTLIER) cc_final: 0.4634 (pp) REVERT: A 409 MET cc_start: 0.7342 (mtp) cc_final: 0.7068 (mtm) REVERT: A 441 ILE cc_start: 0.7706 (mm) cc_final: 0.7497 (mm) REVERT: B 13 LEU cc_start: 0.4899 (OUTLIER) cc_final: 0.4532 (pp) REVERT: B 341 THR cc_start: 0.7504 (p) cc_final: 0.7219 (p) REVERT: B 441 ILE cc_start: 0.7592 (mm) cc_final: 0.7357 (mm) REVERT: C 13 LEU cc_start: 0.4919 (OUTLIER) cc_final: 0.4543 (pp) REVERT: C 330 TYR cc_start: 0.6776 (OUTLIER) cc_final: 0.5236 (t80) REVERT: C 409 MET cc_start: 0.7381 (mtp) cc_final: 0.7121 (mtm) REVERT: C 441 ILE cc_start: 0.7596 (mm) cc_final: 0.7348 (mm) REVERT: D 330 TYR cc_start: 0.6799 (OUTLIER) cc_final: 0.5385 (t80) REVERT: D 409 MET cc_start: 0.7305 (mtp) cc_final: 0.7051 (mtm) outliers start: 35 outliers final: 12 residues processed: 369 average time/residue: 0.5362 time to fit residues: 218.4466 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 : 0.602 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 299 GLN A 350 GLN A 389 ASN A 474 ASN B 157 HIS B 220 ASN B 299 GLN B 301 GLN B 342 GLN B 350 GLN B 389 ASN B 474 ASN C 299 GLN C 342 GLN C 350 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 = 0.3888 r_free = 0.3888 target = 0.155599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.135444 restraints weight = 18056.768| |-----------------------------------------------------------------------------| r_work (start): 0.3718 rms_B_bonded: 2.06 r_work: 0.3634 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7401 moved from start: 0.1587 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= 0.217 Angle : 0.603 8.396 21352 Z= 0.322 Chirality : 0.045 0.163 2364 Planarity : 0.005 0.042 2736 Dihedral : 9.739 58.690 2353 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 4.72 % Allowed : 13.55 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.40 (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 0.021 0.002 TYR D 351 PHE 0.015 0.002 PHE C 24 TRP 0.012 0.002 TRP D 178 HIS 0.009 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00527 (15748) covalent geometry : angle 0.60336 (21352) hydrogen bonds : bond 0.05111 ( 797) hydrogen bonds : angle 5.14451 ( 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 314 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 237 time to evaluate : 0.372 Fit side-chains REVERT: A 13 LEU cc_start: 0.5263 (OUTLIER) cc_final: 0.4978 (pp) REVERT: A 19 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.5983 (mm-40) REVERT: A 156 ARG cc_start: 0.8919 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: A 262 ASN cc_start: 0.7421 (OUTLIER) cc_final: 0.7124 (p0) REVERT: A 325 GLU cc_start: 0.6915 (tt0) cc_final: 0.6368 (pt0) REVERT: A 330 TYR cc_start: 0.7207 (OUTLIER) cc_final: 0.5372 (t80) REVERT: A 341 THR cc_start: 0.7449 (p) cc_final: 0.6610 (p) REVERT: A 399 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8063 (mt-10) REVERT: A 409 MET cc_start: 0.8350 (mtp) cc_final: 0.7686 (mtm) REVERT: A 481 TYR cc_start: 0.7082 (t80) cc_final: 0.6493 (t80) REVERT: A 485 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.6749 (mp0) REVERT: B 13 LEU cc_start: 0.5217 (OUTLIER) cc_final: 0.4895 (pp) REVERT: B 19 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6163 (mm-40) REVERT: B 325 GLU cc_start: 0.6918 (tt0) cc_final: 0.6408 (pt0) REVERT: B 330 TYR cc_start: 0.7187 (OUTLIER) cc_final: 0.6154 (t80) REVERT: B 341 THR cc_start: 0.7499 (p) cc_final: 0.6853 (p) REVERT: B 416 ASP cc_start: 0.5644 (t70) cc_final: 0.5378 (m-30) REVERT: C 13 LEU cc_start: 0.5129 (OUTLIER) cc_final: 0.4830 (pp) REVERT: C 19 GLN cc_start: 0.7061 (OUTLIER) cc_final: 0.5768 (mm-40) REVERT: C 156 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8402 (mtp85) REVERT: C 322 ARG cc_start: 0.7537 (ttm170) cc_final: 0.7226 (mtt-85) REVERT: C 325 GLU cc_start: 0.6697 (tt0) cc_final: 0.6292 (pt0) REVERT: C 409 MET cc_start: 0.8322 (mtp) cc_final: 0.7644 (mtm) REVERT: C 481 TYR cc_start: 0.6999 (t80) cc_final: 0.6468 (t80) REVERT: C 485 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.6704 (mp0) REVERT: D 19 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6251 (mm-40) REVERT: D 102 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7274 (tt) REVERT: D 156 ARG cc_start: 0.8956 (OUTLIER) cc_final: 0.8395 (mtp85) REVERT: D 321 ARG cc_start: 0.7324 (mpt180) cc_final: 0.6989 (mpt90) REVERT: D 409 MET cc_start: 0.8237 (mtp) cc_final: 0.7619 (mtm) REVERT: D 438 ASP cc_start: 0.6632 (m-30) cc_final: 0.5898 (t0) REVERT: D 481 TYR cc_start: 0.6979 (t80) cc_final: 0.6432 (t80) REVERT: D 485 GLU cc_start: 0.7899 (OUTLIER) cc_final: 0.6620 (mp0) outliers start: 77 outliers final: 33 residues processed: 275 average time/residue: 0.5132 time to fit residues: 155.8524 Evaluate side-chains 282 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 231 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 357 LEU Chi-restraints excluded: chain B residue 360 SER 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 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 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 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: 0.8980 chunk 159 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 chunk 172 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 114 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3893 r_free = 0.3893 target = 0.156211 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.136105 restraints weight = 18067.936| |-----------------------------------------------------------------------------| r_work (start): 0.3728 rms_B_bonded: 2.06 r_work: 0.3645 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3539 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1747 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= 0.172 Angle : 0.548 6.904 21352 Z= 0.293 Chirality : 0.043 0.161 2364 Planarity : 0.005 0.042 2736 Dihedral : 8.706 58.516 2344 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.35 % Allowed : 16.68 % Favored : 78.97 % 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 aren not related in a simple way. whole: 0.49 (0.19), residues: 1964 helix: 1.27 (0.18), residues: 864 sheet: -0.05 (0.25), residues: 420 loop : -0.52 (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 covalent geometry : bond 0.00414 (15748) covalent geometry : angle 0.54764 (21352) hydrogen bonds : bond 0.04531 ( 797) hydrogen bonds : angle 4.93138 ( 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: 71 poor density : 240 time to evaluate : 0.568 Fit side-chains REVERT: A 19 GLN cc_start: 0.7044 (OUTLIER) cc_final: 0.5937 (mm-40) REVERT: A 156 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8380 (mtp85) REVERT: A 321 ARG cc_start: 0.6835 (mtm-85) cc_final: 0.6178 (mtp-110) REVERT: A 325 GLU cc_start: 0.6843 (tt0) cc_final: 0.6381 (pt0) REVERT: A 399 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8047 (mt-10) REVERT: A 409 MET cc_start: 0.8261 (mtp) cc_final: 0.7637 (mtm) REVERT: A 481 TYR cc_start: 0.7092 (t80) cc_final: 0.6499 (t80) REVERT: A 485 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: B 19 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.6099 (mm-40) REVERT: B 121 ASN cc_start: 0.7802 (m110) cc_final: 0.7415 (m-40) REVERT: B 321 ARG cc_start: 0.6813 (mtm-85) cc_final: 0.6146 (mtp-110) REVERT: B 325 GLU cc_start: 0.6930 (tt0) cc_final: 0.6386 (pt0) REVERT: B 330 TYR cc_start: 0.7225 (OUTLIER) cc_final: 0.6015 (t80) REVERT: B 341 THR cc_start: 0.7600 (p) cc_final: 0.6914 (p) REVERT: B 416 ASP cc_start: 0.5613 (t70) cc_final: 0.5324 (m-30) REVERT: C 19 GLN cc_start: 0.7058 (OUTLIER) cc_final: 0.5793 (mm-40) REVERT: C 156 ARG cc_start: 0.8939 (OUTLIER) cc_final: 0.8385 (mtp85) REVERT: C 321 ARG cc_start: 0.6770 (mtm-85) cc_final: 0.6154 (mtp-110) REVERT: C 322 ARG cc_start: 0.7601 (ttm170) cc_final: 0.7348 (mtt-85) REVERT: C 325 GLU cc_start: 0.6733 (tt0) cc_final: 0.6274 (pt0) REVERT: C 399 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.8077 (mt-10) REVERT: C 409 MET cc_start: 0.8237 (mtp) cc_final: 0.7570 (mtm) REVERT: D 19 GLN cc_start: 0.7079 (OUTLIER) cc_final: 0.6039 (mm-40) REVERT: D 87 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7663 (mmm160) REVERT: D 102 LEU cc_start: 0.7600 (OUTLIER) cc_final: 0.7263 (tt) REVERT: D 156 ARG cc_start: 0.8961 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: D 409 MET cc_start: 0.8227 (mtp) cc_final: 0.7594 (mtm) REVERT: D 438 ASP cc_start: 0.6414 (m-30) cc_final: 0.5810 (t0) REVERT: D 441 ILE cc_start: 0.7213 (mm) cc_final: 0.7008 (mm) REVERT: D 481 TYR cc_start: 0.6981 (t80) cc_final: 0.6411 (t80) REVERT: D 485 GLU cc_start: 0.7832 (OUTLIER) cc_final: 0.6552 (mp0) outliers start: 71 outliers final: 37 residues processed: 281 average time/residue: 0.5293 time to fit residues: 163.9772 Evaluate side-chains 279 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 229 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 469 PHE Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 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 D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 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: 1.9990 chunk 173 optimal weight: 6.9990 chunk 175 optimal weight: 1.9990 chunk 188 optimal weight: 2.9990 chunk 160 optimal weight: 0.0980 chunk 70 optimal weight: 4.9990 chunk 171 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 166 optimal weight: 4.9990 chunk 121 optimal weight: 0.9990 overall best weight: 1.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3886 r_free = 0.3886 target = 0.155481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.135701 restraints weight = 18044.258| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.00 r_work: 0.3653 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3551 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.1871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15748 Z= 0.180 Angle : 0.548 6.252 21352 Z= 0.293 Chirality : 0.043 0.162 2364 Planarity : 0.005 0.042 2736 Dihedral : 8.315 59.072 2342 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.09 % Allowed : 16.49 % Favored : 78.42 % 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 aren not related in a simple way. whole: 0.44 (0.19), residues: 1964 helix: 1.28 (0.18), residues: 860 sheet: -0.14 (0.25), residues: 420 loop : -0.57 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.023 0.002 TYR B 351 PHE 0.013 0.002 PHE D 290 TRP 0.012 0.001 TRP C 178 HIS 0.007 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00437 (15748) covalent geometry : angle 0.54779 (21352) hydrogen bonds : bond 0.04515 ( 797) hydrogen bonds : angle 4.90727 ( 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 314 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 231 time to evaluate : 0.602 Fit side-chains REVERT: A 19 GLN cc_start: 0.7124 (OUTLIER) cc_final: 0.5954 (mm-40) REVERT: A 156 ARG cc_start: 0.8909 (OUTLIER) cc_final: 0.8328 (mtp85) REVERT: A 321 ARG cc_start: 0.6838 (mtm-85) cc_final: 0.6187 (mtp-110) REVERT: A 325 GLU cc_start: 0.6861 (tt0) cc_final: 0.6389 (pt0) REVERT: A 349 GLU cc_start: 0.6847 (OUTLIER) cc_final: 0.6397 (mp0) REVERT: A 399 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.8050 (mt-10) REVERT: A 409 MET cc_start: 0.8255 (mtp) cc_final: 0.7639 (mtm) REVERT: B 19 GLN cc_start: 0.7021 (OUTLIER) cc_final: 0.6022 (mm-40) REVERT: B 121 ASN cc_start: 0.7709 (m110) cc_final: 0.7289 (m-40) REVERT: B 321 ARG cc_start: 0.6820 (mtm-85) cc_final: 0.6169 (mtp-110) REVERT: B 325 GLU cc_start: 0.6898 (tt0) cc_final: 0.6399 (pt0) REVERT: B 330 TYR cc_start: 0.7124 (OUTLIER) cc_final: 0.5612 (t80) REVERT: B 341 THR cc_start: 0.7638 (p) cc_final: 0.6797 (p) REVERT: B 416 ASP cc_start: 0.5769 (t70) cc_final: 0.5435 (m-30) REVERT: B 485 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7669 (mm-30) REVERT: C 19 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.5837 (mm-40) REVERT: C 156 ARG cc_start: 0.8924 (OUTLIER) cc_final: 0.8365 (mtp85) REVERT: C 321 ARG cc_start: 0.6770 (mtm-85) cc_final: 0.6162 (mtp-110) REVERT: C 325 GLU cc_start: 0.6734 (tt0) cc_final: 0.6292 (pt0) REVERT: C 399 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.8082 (mt-10) REVERT: C 409 MET cc_start: 0.8320 (mtp) cc_final: 0.7670 (mtm) REVERT: D 19 GLN cc_start: 0.7118 (OUTLIER) cc_final: 0.6038 (mm-40) REVERT: D 87 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7666 (mmm160) REVERT: D 102 LEU cc_start: 0.7725 (OUTLIER) cc_final: 0.7407 (tt) REVERT: D 156 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8360 (mtp85) REVERT: D 349 GLU cc_start: 0.6868 (OUTLIER) cc_final: 0.6592 (mp0) REVERT: D 441 ILE cc_start: 0.7208 (mm) cc_final: 0.7006 (mm) outliers start: 83 outliers final: 50 residues processed: 285 average time/residue: 0.4907 time to fit residues: 154.8491 Evaluate side-chains 284 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 220 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 160 ILE Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 349 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 412 LYS Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 209 ILE Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 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 315 ILE Chi-restraints excluded: chain C residue 357 LEU Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 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 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 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: 0.6980 chunk 185 optimal weight: 0.0060 chunk 97 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 156 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 162 optimal weight: 0.9980 chunk 86 optimal weight: 0.8980 overall best weight: 0.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 262 ASN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3915 r_free = 0.3915 target = 0.158157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.138250 restraints weight = 17888.731| |-----------------------------------------------------------------------------| r_work (start): 0.3751 rms_B_bonded: 2.04 r_work: 0.3666 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.1958 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= 0.117 Angle : 0.492 5.756 21352 Z= 0.265 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.041 2736 Dihedral : 7.717 58.801 2340 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 4.11 % Allowed : 17.90 % Favored : 77.99 % 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 aren not related in a simple way. whole: 0.64 (0.20), residues: 1964 helix: 1.48 (0.18), residues: 860 sheet: -0.04 (0.26), residues: 420 loop : -0.52 (0.24), residues: 684 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 D 290 TRP 0.010 0.001 TRP C 453 HIS 0.007 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00264 (15748) covalent geometry : angle 0.49214 (21352) hydrogen bonds : bond 0.03703 ( 797) hydrogen bonds : angle 4.74238 ( 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 302 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 235 time to evaluate : 0.421 Fit side-chains REVERT: A 19 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.5830 (mm-40) REVERT: A 109 MET cc_start: 0.7334 (OUTLIER) cc_final: 0.7049 (ttp) REVERT: A 156 ARG cc_start: 0.8877 (OUTLIER) cc_final: 0.8283 (mtp85) REVERT: A 321 ARG cc_start: 0.6747 (mtm-85) cc_final: 0.6105 (mtp-110) REVERT: A 325 GLU cc_start: 0.6855 (tt0) cc_final: 0.6324 (pt0) REVERT: A 409 MET cc_start: 0.8235 (mtp) cc_final: 0.7625 (mtm) REVERT: B 19 GLN cc_start: 0.7005 (OUTLIER) cc_final: 0.6027 (mm-40) REVERT: B 109 MET cc_start: 0.7315 (OUTLIER) cc_final: 0.7022 (ttp) REVERT: B 121 ASN cc_start: 0.7804 (m110) cc_final: 0.7428 (m-40) REVERT: B 321 ARG cc_start: 0.6735 (mtm-85) cc_final: 0.6101 (mtp-110) REVERT: B 325 GLU cc_start: 0.6832 (tt0) cc_final: 0.6312 (pt0) REVERT: B 330 TYR cc_start: 0.7076 (OUTLIER) cc_final: 0.5619 (t80) REVERT: B 341 THR cc_start: 0.7546 (p) cc_final: 0.6654 (p) REVERT: B 363 LYS cc_start: 0.7337 (mtpp) cc_final: 0.6702 (mmtm) REVERT: B 416 ASP cc_start: 0.5673 (t70) cc_final: 0.5469 (m-30) REVERT: B 485 GLU cc_start: 0.7846 (OUTLIER) cc_final: 0.7585 (mm-30) REVERT: C 19 GLN cc_start: 0.7016 (OUTLIER) cc_final: 0.5772 (mm-40) REVERT: C 121 ASN cc_start: 0.7549 (m110) cc_final: 0.7305 (m-40) REVERT: C 156 ARG cc_start: 0.8893 (OUTLIER) cc_final: 0.8323 (mtp85) REVERT: C 321 ARG cc_start: 0.6696 (mtm-85) cc_final: 0.6091 (mtp-110) REVERT: C 325 GLU cc_start: 0.6685 (tt0) cc_final: 0.6241 (pt0) REVERT: C 399 GLU cc_start: 0.8332 (OUTLIER) cc_final: 0.8073 (mt-10) REVERT: C 409 MET cc_start: 0.8226 (mtp) cc_final: 0.7579 (mtm) REVERT: C 438 ASP cc_start: 0.6174 (m-30) cc_final: 0.5720 (t0) REVERT: D 19 GLN cc_start: 0.7023 (OUTLIER) cc_final: 0.5896 (mm-40) REVERT: D 102 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7355 (tt) REVERT: D 156 ARG cc_start: 0.8900 (OUTLIER) cc_final: 0.8306 (mtp85) REVERT: D 409 MET cc_start: 0.8157 (mtp) cc_final: 0.7516 (mtm) REVERT: D 438 ASP cc_start: 0.6155 (m-30) cc_final: 0.5667 (t0) outliers start: 67 outliers final: 41 residues processed: 277 average time/residue: 0.4866 time to fit residues: 149.8963 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 : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 209 ILE Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 360 SER 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 109 MET Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 156 ARG Chi-restraints excluded: chain B residue 192 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 303 CYS Chi-restraints excluded: chain B residue 330 TYR Chi-restraints excluded: chain B residue 340 VAL 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 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 469 PHE Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 469 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 11 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 chunk 71 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 167 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 139 optimal weight: 6.9990 chunk 190 optimal weight: 0.8980 chunk 117 optimal weight: 4.9990 chunk 122 optimal weight: 5.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 ASN B 110 ASN B 262 ASN B 301 GLN ** B 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 262 ASN C 301 GLN D 110 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3854 r_free = 0.3854 target = 0.152284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.132677 restraints weight = 18041.552| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 1.99 r_work: 0.3620 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3518 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7448 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 15748 Z= 0.292 Angle : 0.649 8.192 21352 Z= 0.345 Chirality : 0.047 0.172 2364 Planarity : 0.005 0.048 2736 Dihedral : 8.367 58.289 2340 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 6.25 % Allowed : 16.49 % Favored : 77.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.17 (0.19), residues: 1964 helix: 1.06 (0.18), residues: 856 sheet: -0.30 (0.25), residues: 408 loop : -0.70 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 131 TYR 0.025 0.003 TYR B 351 PHE 0.018 0.002 PHE C 24 TRP 0.008 0.002 TRP B 29 HIS 0.008 0.002 HIS A 484 Details of bonding type rmsd covalent geometry : bond 0.00724 (15748) covalent geometry : angle 0.64884 (21352) hydrogen bonds : bond 0.05500 ( 797) hydrogen bonds : angle 5.10734 ( 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 320 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 218 time to evaluate : 0.450 Fit side-chains REVERT: A 19 GLN cc_start: 0.7187 (OUTLIER) cc_final: 0.5969 (mm-40) REVERT: A 109 MET cc_start: 0.7530 (OUTLIER) cc_final: 0.7234 (ttp) REVERT: A 156 ARG cc_start: 0.8963 (OUTLIER) cc_final: 0.8363 (mtp85) REVERT: A 321 ARG cc_start: 0.6869 (mtm-85) cc_final: 0.6170 (mtp-110) REVERT: A 325 GLU cc_start: 0.6991 (tt0) cc_final: 0.6460 (pt0) REVERT: A 349 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6594 (mp0) REVERT: A 399 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8008 (mt-10) REVERT: A 485 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.6637 (mp0) REVERT: B 19 GLN cc_start: 0.7153 (OUTLIER) cc_final: 0.6063 (mm-40) REVERT: B 321 ARG cc_start: 0.6856 (mtm-85) cc_final: 0.6159 (mtp-110) REVERT: B 325 GLU cc_start: 0.6990 (tt0) cc_final: 0.6499 (pt0) REVERT: B 330 TYR cc_start: 0.7231 (OUTLIER) cc_final: 0.5453 (t80) REVERT: B 341 THR cc_start: 0.7700 (p) cc_final: 0.6636 (p) REVERT: B 349 GLU cc_start: 0.6874 (OUTLIER) cc_final: 0.6599 (mp0) REVERT: B 485 GLU cc_start: 0.7964 (OUTLIER) cc_final: 0.7704 (mm-30) REVERT: C 19 GLN cc_start: 0.7135 (OUTLIER) cc_final: 0.5883 (mm-40) REVERT: C 102 LEU cc_start: 0.7700 (OUTLIER) cc_final: 0.7387 (tt) REVERT: C 156 ARG cc_start: 0.8962 (OUTLIER) cc_final: 0.8354 (mtp85) REVERT: C 321 ARG cc_start: 0.6804 (mtm-85) cc_final: 0.6148 (mtp-110) REVERT: C 325 GLU cc_start: 0.6729 (tt0) cc_final: 0.6345 (pt0) REVERT: C 349 GLU cc_start: 0.6914 (OUTLIER) cc_final: 0.6421 (mp0) REVERT: C 399 GLU cc_start: 0.8288 (OUTLIER) cc_final: 0.8044 (mt-10) REVERT: C 409 MET cc_start: 0.8376 (mtp) cc_final: 0.7701 (mtm) REVERT: C 485 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.6668 (mp0) REVERT: D 19 GLN cc_start: 0.7210 (OUTLIER) cc_final: 0.6014 (mm-40) REVERT: D 102 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7308 (tt) REVERT: D 156 ARG cc_start: 0.8972 (OUTLIER) cc_final: 0.8416 (mtp85) REVERT: D 349 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6680 (mp0) REVERT: D 399 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: D 485 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.6612 (mp0) outliers start: 102 outliers final: 52 residues processed: 288 average time/residue: 0.5126 time to fit residues: 163.6526 Evaluate side-chains 284 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 210 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 109 MET Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 122 ASP Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 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 349 GLU Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain A residue 485 GLU Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 122 ASP Chi-restraints excluded: chain B residue 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 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 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 461 SER Chi-restraints excluded: chain C residue 485 GLU Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 357 LEU Chi-restraints excluded: chain D residue 360 SER Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 415 ASP Chi-restraints excluded: chain D residue 461 SER Chi-restraints excluded: chain D residue 485 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 105 optimal weight: 1.9990 chunk 63 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 114 optimal weight: 4.9990 chunk 151 optimal weight: 0.5980 chunk 183 optimal weight: 3.9990 chunk 168 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 159 optimal weight: 2.9990 chunk 154 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN B 350 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 = 0.3903 r_free = 0.3903 target = 0.157036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.137461 restraints weight = 17819.680| |-----------------------------------------------------------------------------| r_work (start): 0.3755 rms_B_bonded: 1.98 r_work: 0.3672 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3569 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7374 moved from start: 0.2128 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= 0.122 Angle : 0.501 6.310 21352 Z= 0.271 Chirality : 0.042 0.161 2364 Planarity : 0.004 0.040 2736 Dihedral : 7.629 58.645 2338 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 4.29 % Allowed : 18.95 % Favored : 76.76 % 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 aren not related in a simple way. whole: 0.50 (0.19), residues: 1964 helix: 1.38 (0.18), residues: 856 sheet: -0.15 (0.25), residues: 420 loop : -0.58 (0.24), residues: 688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 322 TYR 0.021 0.002 TYR A 351 PHE 0.011 0.001 PHE C 290 TRP 0.013 0.001 TRP A 453 HIS 0.008 0.001 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00275 (15748) covalent geometry : angle 0.50094 (21352) hydrogen bonds : bond 0.03806 ( 797) hydrogen bonds : angle 4.80444 ( 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 290 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 220 time to evaluate : 0.463 Fit side-chains REVERT: A 19 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.5834 (mm-40) REVERT: A 156 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8326 (mtp85) REVERT: A 321 ARG cc_start: 0.6734 (mtm-85) cc_final: 0.6092 (mtp-110) REVERT: A 325 GLU cc_start: 0.6854 (tt0) cc_final: 0.6358 (pt0) REVERT: A 399 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.8007 (mt-10) REVERT: B 19 GLN cc_start: 0.7007 (OUTLIER) cc_final: 0.5842 (mm-40) REVERT: B 121 ASN cc_start: 0.7737 (m110) cc_final: 0.7424 (m-40) REVERT: B 321 ARG cc_start: 0.6744 (mtm-85) cc_final: 0.6079 (mtp-110) REVERT: B 325 GLU cc_start: 0.6995 (tt0) cc_final: 0.6484 (pt0) REVERT: B 330 TYR cc_start: 0.7129 (OUTLIER) cc_final: 0.5508 (t80) REVERT: B 341 THR cc_start: 0.7645 (p) cc_final: 0.6533 (p) REVERT: B 363 LYS cc_start: 0.7334 (mtpp) cc_final: 0.6769 (mmtm) REVERT: B 416 ASP cc_start: 0.5780 (t70) cc_final: 0.5454 (m-30) REVERT: C 19 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.5874 (mm-40) REVERT: C 102 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7233 (tt) REVERT: C 156 ARG cc_start: 0.8913 (OUTLIER) cc_final: 0.8335 (mtp85) REVERT: C 321 ARG cc_start: 0.6712 (mtm-85) cc_final: 0.6089 (mtp-110) REVERT: C 325 GLU cc_start: 0.6687 (tt0) cc_final: 0.6219 (pt0) REVERT: C 399 GLU cc_start: 0.8260 (OUTLIER) cc_final: 0.8031 (mt-10) REVERT: C 409 MET cc_start: 0.8337 (mtp) cc_final: 0.7693 (mtm) REVERT: C 438 ASP cc_start: 0.6362 (m-30) cc_final: 0.5831 (t0) REVERT: D 19 GLN cc_start: 0.7147 (OUTLIER) cc_final: 0.5915 (mm-40) REVERT: D 102 LEU cc_start: 0.7671 (OUTLIER) cc_final: 0.7319 (tt) REVERT: D 156 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8380 (mtp85) REVERT: D 399 GLU cc_start: 0.8329 (OUTLIER) cc_final: 0.8081 (mt-10) REVERT: D 409 MET cc_start: 0.8102 (mtp) cc_final: 0.7613 (mtm) REVERT: D 438 ASP cc_start: 0.6185 (m-30) cc_final: 0.5697 (t0) outliers start: 70 outliers final: 41 residues processed: 264 average time/residue: 0.4957 time to fit residues: 145.2272 Evaluate side-chains 266 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 212 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 58 GLU Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 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 357 LEU Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 415 ASP Chi-restraints excluded: chain A residue 461 SER Chi-restraints excluded: chain B residue 13 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 114 LEU Chi-restraints excluded: chain B residue 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 102 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 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 58 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 196 random chunks: chunk 39 optimal weight: 3.9990 chunk 150 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 152 optimal weight: 3.9990 chunk 149 optimal weight: 1.9990 chunk 99 optimal weight: 4.9990 chunk 184 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 262 ASN B 301 GLN B 350 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.153030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.133470 restraints weight = 18123.269| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.98 r_work: 0.3629 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3527 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7440 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 15748 Z= 0.272 Angle : 0.624 8.752 21352 Z= 0.333 Chirality : 0.047 0.167 2364 Planarity : 0.005 0.047 2736 Dihedral : 7.948 57.310 2338 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.18 % Favored : 95.82 % Rotamer: Outliers : 5.82 % Allowed : 17.54 % Favored : 76.64 % 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 aren not related in a simple way. whole: 0.17 (0.19), residues: 1964 helix: 1.05 (0.18), residues: 856 sheet: -0.25 (0.25), residues: 408 loop : -0.71 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 131 TYR 0.024 0.002 TYR A 351 PHE 0.016 0.002 PHE C 24 TRP 0.007 0.002 TRP A 29 HIS 0.010 0.002 HIS C 484 Details of bonding type rmsd covalent geometry : bond 0.00677 (15748) covalent geometry : angle 0.62441 (21352) hydrogen bonds : bond 0.05126 ( 797) hydrogen bonds : angle 5.01059 ( 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 302 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 207 time to evaluate : 0.625 Fit side-chains REVERT: A 19 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.5955 (mm-40) REVERT: A 156 ARG cc_start: 0.8944 (OUTLIER) cc_final: 0.8352 (mtp85) REVERT: A 321 ARG cc_start: 0.6837 (mtm-85) cc_final: 0.6151 (mtp-110) REVERT: A 325 GLU cc_start: 0.6996 (tt0) cc_final: 0.6461 (pt0) REVERT: A 349 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6425 (mp0) REVERT: A 399 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8021 (mt-10) REVERT: A 485 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.6667 (mp0) REVERT: B 19 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.5939 (mm-40) REVERT: B 80 MET cc_start: 0.7554 (ttm) cc_final: 0.7252 (ttm) REVERT: B 102 LEU cc_start: 0.7743 (OUTLIER) cc_final: 0.7436 (tt) REVERT: B 321 ARG cc_start: 0.6841 (mtm-85) cc_final: 0.6148 (mtp-110) REVERT: B 325 GLU cc_start: 0.7032 (tt0) cc_final: 0.6489 (pt0) REVERT: B 330 TYR cc_start: 0.7284 (OUTLIER) cc_final: 0.5424 (t80) REVERT: B 341 THR cc_start: 0.7709 (p) cc_final: 0.6476 (p) REVERT: B 416 ASP cc_start: 0.5890 (t70) cc_final: 0.5515 (m-30) REVERT: C 19 GLN cc_start: 0.7180 (OUTLIER) cc_final: 0.5903 (mm-40) REVERT: C 80 MET cc_start: 0.7571 (ttm) cc_final: 0.7261 (ttm) REVERT: C 102 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7366 (tt) REVERT: C 156 ARG cc_start: 0.8957 (OUTLIER) cc_final: 0.8363 (mtp85) REVERT: C 321 ARG cc_start: 0.6794 (mtm-85) cc_final: 0.6128 (mtp-110) REVERT: C 325 GLU cc_start: 0.6727 (tt0) cc_final: 0.6258 (pt0) REVERT: C 349 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6340 (mp0) REVERT: C 399 GLU cc_start: 0.8287 (OUTLIER) cc_final: 0.8057 (mt-10) REVERT: C 409 MET cc_start: 0.8376 (mtp) cc_final: 0.7698 (mtm) REVERT: D 19 GLN cc_start: 0.7218 (OUTLIER) cc_final: 0.5945 (mm-40) REVERT: D 80 MET cc_start: 0.7536 (ttm) cc_final: 0.7240 (ttm) REVERT: D 102 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7392 (tt) REVERT: D 156 ARG cc_start: 0.8945 (OUTLIER) cc_final: 0.8352 (mtp85) REVERT: D 349 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6470 (mp0) REVERT: D 399 GLU cc_start: 0.8364 (OUTLIER) cc_final: 0.8116 (mt-10) outliers start: 95 outliers final: 46 residues processed: 271 average time/residue: 0.4961 time to fit residues: 149.2087 Evaluate side-chains 268 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 204 time to evaluate : 0.389 ------------------------------------------------------------------------------- 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 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 A residue 485 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 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 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 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 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 209 ILE Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 303 CYS Chi-restraints excluded: chain D residue 349 GLU Chi-restraints excluded: chain D residue 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: 0.7980 chunk 195 optimal weight: 1.9990 chunk 170 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 106 optimal weight: 0.9990 chunk 10 optimal weight: 0.7980 chunk 190 optimal weight: 0.9990 chunk 172 optimal weight: 0.7980 chunk 64 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 301 GLN B 350 GLN C 301 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.156302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.136697 restraints weight = 17819.192| |-----------------------------------------------------------------------------| r_work (start): 0.3749 rms_B_bonded: 1.98 r_work: 0.3667 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3566 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3566 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15748 Z= 0.136 Angle : 0.519 6.707 21352 Z= 0.280 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.039 2736 Dihedral : 7.578 58.462 2338 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 3.86 % Allowed : 19.68 % Favored : 76.46 % 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 aren not related in a simple way. whole: 0.43 (0.19), residues: 1964 helix: 1.29 (0.18), residues: 860 sheet: -0.16 (0.25), residues: 420 loop : -0.60 (0.24), residues: 684 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 131 TYR 0.021 0.002 TYR A 351 PHE 0.012 0.001 PHE D 411 TRP 0.008 0.001 TRP C 178 HIS 0.011 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00321 (15748) covalent geometry : angle 0.51851 (21352) hydrogen bonds : bond 0.03937 ( 797) hydrogen bonds : angle 4.80231 ( 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 273 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 210 time to evaluate : 0.643 Fit side-chains REVERT: A 19 GLN cc_start: 0.7159 (OUTLIER) cc_final: 0.5875 (mm-40) REVERT: A 156 ARG cc_start: 0.8908 (OUTLIER) cc_final: 0.8342 (mtp85) REVERT: A 321 ARG cc_start: 0.6786 (mtm-85) cc_final: 0.6108 (mtp-110) REVERT: A 325 GLU cc_start: 0.6865 (tt0) cc_final: 0.6367 (pt0) REVERT: A 399 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.8009 (mt-10) REVERT: B 19 GLN cc_start: 0.7098 (OUTLIER) cc_final: 0.5932 (mm-40) REVERT: B 321 ARG cc_start: 0.6755 (mtm-85) cc_final: 0.6085 (mtp-110) REVERT: B 325 GLU cc_start: 0.7001 (tt0) cc_final: 0.6465 (pt0) REVERT: B 330 TYR cc_start: 0.7250 (OUTLIER) cc_final: 0.5580 (t80) REVERT: B 341 THR cc_start: 0.7656 (p) cc_final: 0.6357 (p) REVERT: B 363 LYS cc_start: 0.7455 (mtpp) cc_final: 0.6793 (mmtm) REVERT: B 416 ASP cc_start: 0.5819 (t70) cc_final: 0.5457 (m-30) REVERT: C 19 GLN cc_start: 0.7108 (OUTLIER) cc_final: 0.5872 (mm-40) REVERT: C 102 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.7239 (tt) REVERT: C 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8337 (mtp85) REVERT: C 321 ARG cc_start: 0.6716 (mtm-85) cc_final: 0.6069 (mtp-110) REVERT: C 325 GLU cc_start: 0.6705 (tt0) cc_final: 0.6255 (pt0) REVERT: C 399 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.8042 (mt-10) REVERT: C 409 MET cc_start: 0.8341 (mtp) cc_final: 0.7691 (mtm) REVERT: D 19 GLN cc_start: 0.7176 (OUTLIER) cc_final: 0.5919 (mm-40) REVERT: D 102 LEU cc_start: 0.7644 (OUTLIER) cc_final: 0.7296 (tt) REVERT: D 156 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8346 (mtp85) REVERT: D 399 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8065 (mt-10) REVERT: D 438 ASP cc_start: 0.6176 (m-30) cc_final: 0.5702 (t0) outliers start: 63 outliers final: 36 residues processed: 250 average time/residue: 0.5161 time to fit residues: 142.9882 Evaluate side-chains 256 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 207 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 LEU Chi-restraints excluded: chain A residue 19 GLN Chi-restraints excluded: chain A residue 114 LEU Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain A residue 245 THR Chi-restraints excluded: chain A residue 303 CYS Chi-restraints excluded: chain A residue 360 SER Chi-restraints excluded: chain A residue 399 GLU Chi-restraints excluded: chain A residue 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 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 102 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 122 ASP Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 303 CYS 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: 0.8980 chunk 194 optimal weight: 4.9990 chunk 161 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 159 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 117 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 18 optimal weight: 0.9980 chunk 41 optimal weight: 3.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 69 GLN B 262 ASN B 301 GLN B 350 GLN C 69 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.155478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.135894 restraints weight = 17958.541| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.98 r_work: 0.3655 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3554 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7396 moved from start: 0.2205 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= 0.175 Angle : 0.544 6.912 21352 Z= 0.293 Chirality : 0.043 0.165 2364 Planarity : 0.005 0.039 2736 Dihedral : 7.590 59.828 2338 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 3.80 % Allowed : 19.87 % 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 aren not related in a simple way. whole: 0.38 (0.19), residues: 1964 helix: 1.23 (0.18), residues: 860 sheet: -0.18 (0.25), residues: 420 loop : -0.61 (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 A 351 PHE 0.013 0.002 PHE D 411 TRP 0.007 0.001 TRP C 178 HIS 0.013 0.002 HIS B 484 Details of bonding type rmsd covalent geometry : bond 0.00425 (15748) covalent geometry : angle 0.54421 (21352) hydrogen bonds : bond 0.04257 ( 797) hydrogen bonds : angle 4.83873 ( 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 267 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 205 time to evaluate : 0.404 Fit side-chains REVERT: A 19 GLN cc_start: 0.7183 (OUTLIER) cc_final: 0.5901 (mm-40) REVERT: A 321 ARG cc_start: 0.6798 (mtm-85) cc_final: 0.6112 (mtp-110) REVERT: A 325 GLU cc_start: 0.6925 (tt0) cc_final: 0.6397 (pt0) REVERT: A 399 GLU cc_start: 0.8262 (OUTLIER) cc_final: 0.8028 (mt-10) REVERT: B 19 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.5999 (mm-40) REVERT: B 80 MET cc_start: 0.7469 (ttm) cc_final: 0.7132 (ttm) REVERT: B 321 ARG cc_start: 0.6779 (mtm-85) cc_final: 0.6099 (mtp-110) REVERT: B 325 GLU cc_start: 0.7053 (tt0) cc_final: 0.6485 (pt0) REVERT: B 330 TYR cc_start: 0.7254 (OUTLIER) cc_final: 0.5549 (t80) REVERT: B 341 THR cc_start: 0.7661 (p) cc_final: 0.6330 (p) REVERT: B 363 LYS cc_start: 0.7458 (mtpp) cc_final: 0.6787 (mmtm) REVERT: B 416 ASP cc_start: 0.5854 (t70) cc_final: 0.5483 (m-30) REVERT: C 19 GLN cc_start: 0.7113 (OUTLIER) cc_final: 0.5877 (mm-40) REVERT: C 80 MET cc_start: 0.7487 (ttm) cc_final: 0.7145 (ttm) REVERT: C 102 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7263 (tt) REVERT: C 156 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8360 (mtp85) REVERT: C 321 ARG cc_start: 0.6725 (mtm-85) cc_final: 0.6074 (mtp-110) REVERT: C 325 GLU cc_start: 0.6700 (tt0) cc_final: 0.6241 (pt0) REVERT: C 399 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8069 (mt-10) REVERT: C 409 MET cc_start: 0.8360 (mtp) cc_final: 0.7689 (mtm) REVERT: D 19 GLN cc_start: 0.7192 (OUTLIER) cc_final: 0.5937 (mm-40) REVERT: D 58 GLU cc_start: 0.6856 (pm20) cc_final: 0.6636 (pm20) REVERT: D 80 MET cc_start: 0.7420 (ttm) cc_final: 0.7102 (ttm) REVERT: D 102 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7305 (tt) REVERT: D 156 ARG cc_start: 0.8916 (OUTLIER) cc_final: 0.8352 (mtp85) REVERT: D 399 GLU cc_start: 0.8354 (OUTLIER) cc_final: 0.8104 (mt-10) REVERT: D 438 ASP cc_start: 0.6180 (m-30) cc_final: 0.5711 (t0) outliers start: 62 outliers final: 39 residues processed: 246 average time/residue: 0.5480 time to fit residues: 148.2253 Evaluate side-chains 258 residues out of total 1632 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 207 time to evaluate : 0.423 ------------------------------------------------------------------------------- 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 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 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 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 340 VAL 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 156 ARG Chi-restraints excluded: chain C residue 192 VAL Chi-restraints excluded: chain C residue 245 THR Chi-restraints excluded: chain C residue 303 CYS Chi-restraints excluded: chain C residue 360 SER Chi-restraints excluded: chain C residue 399 GLU Chi-restraints excluded: chain C residue 415 ASP Chi-restraints excluded: chain C residue 417 VAL Chi-restraints excluded: chain C residue 461 SER Chi-restraints excluded: chain C residue 488 GLU Chi-restraints excluded: chain D residue 13 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 114 LEU Chi-restraints excluded: chain D residue 122 ASP Chi-restraints excluded: chain D residue 156 ARG Chi-restraints excluded: chain D residue 192 VAL Chi-restraints excluded: chain D residue 245 THR Chi-restraints excluded: chain D residue 262 ASN Chi-restraints excluded: chain D residue 303 CYS 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: 2.9990 chunk 174 optimal weight: 0.8980 chunk 118 optimal weight: 0.1980 chunk 65 optimal weight: 0.9980 chunk 172 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 1 optimal weight: 2.9990 chunk 187 optimal weight: 0.7980 chunk 55 optimal weight: 2.9990 chunk 179 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 GLN A 350 GLN B 69 GLN B 301 GLN B 350 GLN C 69 GLN C 262 ASN C 301 GLN D 69 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.157208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.137665 restraints weight = 17658.093| |-----------------------------------------------------------------------------| r_work (start): 0.3759 rms_B_bonded: 1.97 r_work: 0.3678 rms_B_bonded: 2.33 restraints_weight: 0.5000 r_work: 0.3577 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2231 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= 0.126 Angle : 0.511 6.378 21352 Z= 0.276 Chirality : 0.042 0.162 2364 Planarity : 0.004 0.039 2736 Dihedral : 7.365 58.847 2338 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 4.05 % Allowed : 19.80 % 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 aren not related in a simple way. whole: 0.62 (0.20), residues: 1964 helix: 1.39 (0.18), residues: 860 sheet: 0.07 (0.26), residues: 412 loop : -0.52 (0.24), residues: 692 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 131 TYR 0.020 0.001 TYR A 351 PHE 0.011 0.001 PHE D 411 TRP 0.009 0.001 TRP C 178 HIS 0.014 0.002 HIS D 484 Details of bonding type rmsd covalent geometry : bond 0.00294 (15748) covalent geometry : angle 0.51099 (21352) hydrogen bonds : bond 0.03740 ( 797) hydrogen bonds : angle 4.75412 ( 2283) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4446.50 seconds wall clock time: 76 minutes 40.20 seconds (4600.20 seconds total)