Starting phenix.real_space_refine on Fri Sep 11 08:57:54 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.map" restraint_files = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kku_0703/09_2026/6kku_0703.cif" } resolution = 3.5 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= 0.003 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 S 68 5.16 5 Cl 2 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 8412 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' CL': 1, 'DU0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 38 Unusual residues: {' CL': 1, 'DU0': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.91, per 1000 atoms: 0.23 Number of scatterers: 8412 At special positions: 0 Unit cell: (78.11, 101.65, 102.72, 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) Cl 2 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.03 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.03 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 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=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 322.0 milliseconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 4 sheets defined 69.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.18 Creating SS restraints... Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.916A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 141 through 176 removed outlier: 7.212A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N CYS A 162 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU A 166 " --> pdb=" O CYS A 162 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 193 removed outlier: 3.977A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.522A pdb=" N GLY A 198 " --> pdb=" O GLY A 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.589A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 298 Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.526A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 removed outlier: 3.567A pdb=" N ASN A 360 " --> pdb=" O TYR A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.565A pdb=" N LEU A 376 " --> pdb=" O ALA A 372 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 removed outlier: 3.908A pdb=" N SER A 407 " --> pdb=" O LEU A 404 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.650A pdb=" N LEU A 423 " --> pdb=" O SER A 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.633A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.686A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.178A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 536 Proline residue: A 527 - end of helix removed outlier: 3.540A pdb=" N ASP A 536 " --> pdb=" O ALA A 532 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.406A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.895A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 567 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix removed outlier: 3.751A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.741A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.508A pdb=" N ALA A 638 " --> pdb=" O SER A 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.916A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 141 through 176 removed outlier: 7.212A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 8.871A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N CYS B 162 " --> pdb=" O LEU B 158 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU B 166 " --> pdb=" O CYS B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 193 removed outlier: 3.976A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.522A pdb=" N GLY B 198 " --> pdb=" O GLY B 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.589A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 298 Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.526A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 removed outlier: 3.566A pdb=" N ASN B 360 " --> pdb=" O TYR B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.566A pdb=" N LEU B 376 " --> pdb=" O ALA B 372 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.908A pdb=" N SER B 407 " --> pdb=" O LEU B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.649A pdb=" N LEU B 423 " --> pdb=" O SER B 419 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.632A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.686A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.179A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 536 Proline residue: B 527 - end of helix removed outlier: 3.539A pdb=" N ASP B 536 " --> pdb=" O ALA B 532 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.405A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.895A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU B 567 " --> pdb=" O LEU B 563 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix removed outlier: 3.751A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.740A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.508A pdb=" N ALA B 638 " --> pdb=" O SER B 634 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329 486 hydrogen bonds defined for protein. 1386 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: 1.05 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.47: 2313 1.47 - 1.60: 3735 1.60 - 1.72: 0 1.72 - 1.85: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.410 1.503 -0.093 2.00e-02 2.50e+03 2.17e+01 bond pdb=" C1 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BGC J 1 " pdb=" O5 BGC J 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.410 1.485 -0.075 2.00e-02 2.50e+03 1.39e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 11086 1.95 - 3.89: 548 3.89 - 5.84: 110 5.84 - 7.79: 39 7.79 - 9.73: 11 Bond angle restraints: 11794 Sorted by residual: angle pdb=" CA PRO A 230 " pdb=" C PRO A 230 " pdb=" N PRO A 231 " ideal model delta sigma weight residual 117.93 122.96 -5.03 1.20e+00 6.94e-01 1.75e+01 angle pdb=" CA PRO B 230 " pdb=" C PRO B 230 " pdb=" N PRO B 231 " ideal model delta sigma weight residual 117.93 122.90 -4.97 1.20e+00 6.94e-01 1.72e+01 angle pdb=" N VAL A 490 " pdb=" CA VAL A 490 " pdb=" C VAL A 490 " ideal model delta sigma weight residual 106.53 111.67 -5.14 1.41e+00 5.03e-01 1.33e+01 angle pdb=" N PHE A 428 " pdb=" CA PHE A 428 " pdb=" C PHE A 428 " ideal model delta sigma weight residual 113.16 118.28 -5.12 1.42e+00 4.96e-01 1.30e+01 angle pdb=" N PHE B 428 " pdb=" CA PHE B 428 " pdb=" C PHE B 428 " ideal model delta sigma weight residual 113.16 118.28 -5.12 1.42e+00 4.96e-01 1.30e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 4872 34.22 - 68.43: 34 68.43 - 102.65: 2 102.65 - 136.86: 2 136.86 - 171.08: 2 Dihedral angle restraints: 4912 sinusoidal: 1830 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A1106 " pdb=" C24 DU0 A1106 " pdb=" C25 DU0 A1106 " pdb=" O23 DU0 A1106 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C26 DU0 B1108 " pdb=" C24 DU0 B1108 " pdb=" C25 DU0 B1108 " pdb=" O23 DU0 B1108 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" CA VAL A 268 " pdb=" C VAL A 268 " pdb=" N GLY A 269 " pdb=" CA GLY A 269 " ideal model delta harmonic sigma weight residual -180.00 -159.74 -20.26 0 5.00e+00 4.00e-02 1.64e+01 ... (remaining 4909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 1218 0.080 - 0.160: 231 0.160 - 0.240: 15 0.240 - 0.319: 0 0.319 - 0.399: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 312 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.80 0.40 2.00e-01 2.50e+01 3.97e+00 chirality pdb=" C1 GLC F 2 " pdb=" O4 BGC F 1 " pdb=" C2 GLC F 2 " pdb=" O5 GLC F 2 " both_signs ideal model delta sigma weight residual False 2.40 2.37 0.03 2.00e-02 2.50e+03 1.68e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.13e+00 pdb=" N PRO B 409 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.048 5.00e-02 4.00e+02 7.13e-02 8.12e+00 pdb=" N PRO A 409 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 467 " -0.016 2.00e-02 2.50e+03 1.66e-02 4.81e+00 pdb=" CG PHE A 467 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 467 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 467 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 PHE A 467 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 467 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 467 " -0.001 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1782 2.77 - 3.31: 7841 3.31 - 3.84: 13265 3.84 - 4.37: 14998 4.37 - 4.90: 26580 Nonbonded interactions: 64466 Sorted by model distance: nonbonded pdb=" OH TYR A 292 " pdb=" OG SER A 468 " model vdw 2.243 3.040 nonbonded pdb=" OH TYR B 292 " pdb=" OG SER B 468 " model vdw 2.244 3.040 nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.344 3.040 nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.345 3.040 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 3.040 ... (remaining 64461 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: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.600 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 8.090 Find NCS groups from input model: 0.110 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: 0.000 Load rotamer database and sin/cos tables:1.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 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 : 0.009 0.093 8648 Z= 0.407 Angle : 1.158 14.844 11842 Z= 0.558 Chirality : 0.060 0.399 1466 Planarity : 0.008 0.071 1404 Dihedral : 10.881 171.079 2926 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.36 (0.21), residues: 1070 helix: -1.68 (0.16), residues: 622 sheet: None (None), residues: 0 loop : -2.97 (0.25), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 445 TYR 0.025 0.003 TYR A 292 PHE 0.039 0.004 PHE A 467 TRP 0.031 0.003 TRP A 339 HIS 0.006 0.001 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00913 / 0.40 ( 8626) covalent geometry : angle 1.06858 / 0.54 (11794) SS BOND : bond 0.00252 / 0.17 ( 6) SS BOND : angle 2.54088 / 1.22 ( 12) hydrogen bonds : bond 0.16407 / 10.38 ( 486) hydrogen bonds : angle 6.16497 / 4.52 ( 1386) Misc. bond : bond 0.00749 / 0.44 ( 4) link_ALPHA1-4 : bond 0.05558 / 3.29 ( 4) link_ALPHA1-4 : angle 2.30409 / 1.31 ( 12) link_BETA1-4 : bond 0.02270 / 1.39 ( 4) link_BETA1-4 : angle 10.74578 / 6.08 ( 12) link_NAG-ASN : bond 0.00864 / 0.50 ( 4) link_NAG-ASN : angle 8.61615 / 5.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 293 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.243 Fit side-chains REVERT: A 180 VAL cc_start: 0.8404 (t) cc_final: 0.8171 (t) REVERT: A 297 LYS cc_start: 0.8587 (tttm) cc_final: 0.7946 (mmtm) REVERT: A 405 LYS cc_start: 0.8370 (tttp) cc_final: 0.7860 (ttpp) REVERT: B 144 MET cc_start: 0.8255 (ttm) cc_final: 0.7999 (ttt) REVERT: B 176 THR cc_start: 0.8818 (p) cc_final: 0.8436 (t) REVERT: B 297 LYS cc_start: 0.8699 (tttm) cc_final: 0.7868 (mmtm) REVERT: B 405 LYS cc_start: 0.8357 (tttp) cc_final: 0.7862 (ttpp) REVERT: B 484 ASP cc_start: 0.8380 (m-30) cc_final: 0.8071 (m-30) outliers start: 0 outliers final: 0 residues processed: 293 average time/residue: 0.0877 time to fit residues: 34.9498 Evaluate side-chains 139 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 4.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 8.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 531 GLN B 130 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.132272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.108551 restraints weight = 13900.406| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.111835 restraints weight = 7865.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.113949 restraints weight = 5538.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.115277 restraints weight = 4463.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.116018 restraints weight = 3895.003| |-----------------------------------------------------------------------------| r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 8648 Z= 0.163 Angle : 0.723 9.446 11842 Z= 0.340 Chirality : 0.044 0.184 1466 Planarity : 0.005 0.066 1404 Dihedral : 10.044 163.047 1194 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 2.49 % Allowed : 10.09 % Favored : 87.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.24), residues: 1070 helix: 0.62 (0.20), residues: 638 sheet: None (None), residues: 0 loop : -2.62 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.018 0.002 TYR A 613 PHE 0.014 0.002 PHE B 428 TRP 0.016 0.001 TRP A 616 HIS 0.003 0.001 HIS A 344 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.16 ( 8626) covalent geometry : angle 0.67774 / 0.33 (11794) SS BOND : bond 0.00132 / 0.08 ( 6) SS BOND : angle 1.40012 / 0.64 ( 12) hydrogen bonds : bond 0.04898 / 3.21 ( 486) hydrogen bonds : angle 4.08771 / 3.00 ( 1386) Misc. bond : bond 0.00074 / 0.04 ( 4) link_ALPHA1-4 : bond 0.00246 / 0.15 ( 4) link_ALPHA1-4 : angle 1.55770 / 0.75 ( 12) link_BETA1-4 : bond 0.01155 / 0.71 ( 4) link_BETA1-4 : angle 6.34702 / 3.51 ( 12) link_NAG-ASN : bond 0.00194 / 0.11 ( 4) link_NAG-ASN : angle 4.46187 / 2.73 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 162 time to evaluate : 0.366 Fit side-chains REVERT: A 537 ASN cc_start: 0.8433 (OUTLIER) cc_final: 0.8196 (t0) REVERT: B 130 GLN cc_start: 0.8077 (tt0) cc_final: 0.7720 (tt0) REVERT: B 380 LEU cc_start: 0.8756 (OUTLIER) cc_final: 0.8494 (mt) REVERT: B 490 VAL cc_start: 0.8291 (OUTLIER) cc_final: 0.8002 (p) REVERT: B 537 ASN cc_start: 0.8383 (OUTLIER) cc_final: 0.8050 (t0) outliers start: 22 outliers final: 7 residues processed: 179 average time/residue: 0.0761 time to fit residues: 20.1937 Evaluate side-chains 146 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 135 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 469 SER Chi-restraints excluded: chain A residue 537 ASN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109089 restraints weight = 13729.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.112318 restraints weight = 7791.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.114417 restraints weight = 5522.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115679 restraints weight = 4466.570| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.116582 restraints weight = 3922.860| |-----------------------------------------------------------------------------| r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8648 Z= 0.139 Angle : 0.698 10.683 11842 Z= 0.330 Chirality : 0.044 0.309 1466 Planarity : 0.004 0.054 1404 Dihedral : 9.759 158.254 1194 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.83 % Allowed : 11.90 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.09 (0.25), residues: 1070 helix: 1.31 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -2.29 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 445 TYR 0.016 0.001 TYR B 613 PHE 0.025 0.001 PHE A 261 TRP 0.016 0.001 TRP B 616 HIS 0.005 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00320 / 0.14 ( 8626) covalent geometry : angle 0.65481 / 0.32 (11794) SS BOND : bond 0.00516 / 0.30 ( 6) SS BOND : angle 1.42357 / 0.69 ( 12) hydrogen bonds : bond 0.04499 / 2.94 ( 486) hydrogen bonds : angle 4.02935 / 2.97 ( 1386) Misc. bond : bond 0.00030 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00336 / 0.20 ( 4) link_ALPHA1-4 : angle 1.09007 / 0.57 ( 12) link_BETA1-4 : bond 0.01219 / 0.74 ( 4) link_BETA1-4 : angle 6.34478 / 3.53 ( 12) link_NAG-ASN : bond 0.00144 / 0.08 ( 4) link_NAG-ASN : angle 4.00456 / 2.53 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 151 time to evaluate : 0.284 Fit side-chains revert: symmetry clash REVERT: B 130 GLN cc_start: 0.8077 (tt0) cc_final: 0.7693 (tt0) REVERT: B 251 MET cc_start: 0.8677 (mmm) cc_final: 0.8476 (mtp) REVERT: B 380 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8287 (mt) REVERT: B 405 LYS cc_start: 0.7919 (tttp) cc_final: 0.7589 (ttpp) REVERT: B 410 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8317 (tt) REVERT: B 537 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8207 (t0) outliers start: 25 outliers final: 11 residues processed: 167 average time/residue: 0.0758 time to fit residues: 18.6481 Evaluate side-chains 149 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 135 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 54 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 39 optimal weight: 0.9980 chunk 64 optimal weight: 0.0770 chunk 12 optimal weight: 1.9990 chunk 84 optimal weight: 0.0970 chunk 8 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 75 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 overall best weight: 0.7738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 493 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.134450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.110301 restraints weight = 13905.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.113719 restraints weight = 7777.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.115941 restraints weight = 5428.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.117155 restraints weight = 4342.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.118147 restraints weight = 3813.197| |-----------------------------------------------------------------------------| r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8648 Z= 0.121 Angle : 0.665 8.980 11842 Z= 0.311 Chirality : 0.043 0.249 1466 Planarity : 0.004 0.045 1404 Dihedral : 9.487 152.461 1194 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.72 % Allowed : 12.47 % Favored : 84.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.26), residues: 1070 helix: 1.80 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.17 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 445 TYR 0.016 0.001 TYR B 613 PHE 0.024 0.001 PHE B 261 TRP 0.017 0.001 TRP B 616 HIS 0.004 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 ( 8626) covalent geometry : angle 0.62454 / 0.30 (11794) SS BOND : bond 0.00510 / 0.30 ( 6) SS BOND : angle 1.82387 / 0.89 ( 12) hydrogen bonds : bond 0.04093 / 2.67 ( 486) hydrogen bonds : angle 3.82613 / 2.82 ( 1386) Misc. bond : bond 0.00012 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00331 / 0.20 ( 4) link_ALPHA1-4 : angle 1.11101 / 0.61 ( 12) link_BETA1-4 : bond 0.01259 / 0.77 ( 4) link_BETA1-4 : angle 5.96478 / 3.30 ( 12) link_NAG-ASN : bond 0.00233 / 0.14 ( 4) link_NAG-ASN : angle 3.62038 / 2.31 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 153 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8219 (ttm) cc_final: 0.7767 (ttt) REVERT: A 493 ASN cc_start: 0.8491 (m110) cc_final: 0.8282 (m110) REVERT: B 130 GLN cc_start: 0.8035 (tt0) cc_final: 0.7707 (tt0) REVERT: B 380 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8303 (mt) REVERT: B 405 LYS cc_start: 0.7889 (tttp) cc_final: 0.7565 (ttpp) REVERT: B 410 LEU cc_start: 0.8697 (OUTLIER) cc_final: 0.8319 (tt) outliers start: 24 outliers final: 14 residues processed: 168 average time/residue: 0.0712 time to fit residues: 17.6056 Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 134 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 469 SER Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 602 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 38 optimal weight: 0.6980 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 95 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 51 optimal weight: 5.9990 chunk 53 optimal weight: 9.9990 chunk 23 optimal weight: 20.0000 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.134720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.110456 restraints weight = 13709.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.113773 restraints weight = 7799.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.115940 restraints weight = 5522.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.117229 restraints weight = 4450.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.118167 restraints weight = 3905.864| |-----------------------------------------------------------------------------| r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8648 Z= 0.120 Angle : 0.646 8.466 11842 Z= 0.304 Chirality : 0.043 0.233 1466 Planarity : 0.004 0.041 1404 Dihedral : 9.232 144.873 1194 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.49 % Allowed : 15.19 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.72 (0.26), residues: 1070 helix: 2.05 (0.21), residues: 638 sheet: None (None), residues: 0 loop : -2.10 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.014 0.001 TYR B 613 PHE 0.011 0.001 PHE A 428 TRP 0.013 0.001 TRP A 616 HIS 0.002 0.000 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 ( 8626) covalent geometry : angle 0.60820 / 0.29 (11794) SS BOND : bond 0.00451 / 0.27 ( 6) SS BOND : angle 1.54342 / 0.78 ( 12) hydrogen bonds : bond 0.03908 / 2.55 ( 486) hydrogen bonds : angle 3.72573 / 2.73 ( 1386) Misc. bond : bond 0.00019 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00346 / 0.20 ( 4) link_ALPHA1-4 : angle 1.00267 / 0.53 ( 12) link_BETA1-4 : bond 0.01283 / 0.79 ( 4) link_BETA1-4 : angle 5.73074 / 3.17 ( 12) link_NAG-ASN : bond 0.00210 / 0.12 ( 4) link_NAG-ASN : angle 3.48999 / 2.27 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 145 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 380 LEU cc_start: 0.8611 (mt) cc_final: 0.8343 (mt) REVERT: A 594 LEU cc_start: 0.9089 (tp) cc_final: 0.8826 (tp) REVERT: B 130 GLN cc_start: 0.8006 (tt0) cc_final: 0.7730 (tt0) REVERT: B 262 MET cc_start: 0.8186 (mtm) cc_final: 0.7975 (mtt) REVERT: B 380 LEU cc_start: 0.8742 (OUTLIER) cc_final: 0.8375 (mt) REVERT: B 405 LYS cc_start: 0.7872 (tttp) cc_final: 0.7543 (ttpp) REVERT: B 410 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8376 (tt) REVERT: B 594 LEU cc_start: 0.9077 (tp) cc_final: 0.8803 (tp) outliers start: 22 outliers final: 16 residues processed: 157 average time/residue: 0.0738 time to fit residues: 16.9107 Evaluate side-chains 153 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 135 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 410 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 23 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 chunk 87 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 103 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 20.0000 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 493 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.133345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.109172 restraints weight = 13774.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.112405 restraints weight = 7859.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114537 restraints weight = 5582.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.115832 restraints weight = 4510.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.116595 restraints weight = 3953.307| |-----------------------------------------------------------------------------| r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8648 Z= 0.144 Angle : 0.674 8.217 11842 Z= 0.315 Chirality : 0.044 0.234 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.077 138.905 1194 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.51 % Allowed : 14.63 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1070 helix: 2.12 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -2.06 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.016 0.001 TYR B 613 PHE 0.013 0.001 PHE A 428 TRP 0.008 0.001 TRP B 339 HIS 0.003 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.14 ( 8626) covalent geometry : angle 0.63702 / 0.31 (11794) SS BOND : bond 0.00476 / 0.28 ( 6) SS BOND : angle 1.60453 / 0.83 ( 12) hydrogen bonds : bond 0.04077 / 2.67 ( 486) hydrogen bonds : angle 3.75237 / 2.75 ( 1386) Misc. bond : bond 0.00016 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00294 / 0.18 ( 4) link_ALPHA1-4 : angle 1.07111 / 0.57 ( 12) link_BETA1-4 : bond 0.01281 / 0.78 ( 4) link_BETA1-4 : angle 5.70980 / 3.18 ( 12) link_NAG-ASN : bond 0.00092 / 0.05 ( 4) link_NAG-ASN : angle 3.64207 / 2.39 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 143 time to evaluate : 0.382 Fit side-chains REVERT: A 380 LEU cc_start: 0.8681 (mt) cc_final: 0.8437 (mt) REVERT: A 594 LEU cc_start: 0.9080 (tp) cc_final: 0.8825 (tt) REVERT: B 130 GLN cc_start: 0.8043 (tt0) cc_final: 0.7785 (tt0) REVERT: B 380 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8423 (mt) REVERT: B 594 LEU cc_start: 0.9080 (tp) cc_final: 0.8848 (tt) outliers start: 31 outliers final: 21 residues processed: 161 average time/residue: 0.0737 time to fit residues: 17.6188 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 134 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 GLN Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 602 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 334 VAL Chi-restraints excluded: chain B residue 380 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 555 THR Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 600 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 71 optimal weight: 0.0970 chunk 104 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 86 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 6.9990 chunk 72 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.135167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.110854 restraints weight = 13793.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3347 r_free = 0.3347 target = 0.114190 restraints weight = 7805.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116393 restraints weight = 5517.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.117606 restraints weight = 4433.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.118571 restraints weight = 3902.155| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8648 Z= 0.118 Angle : 0.659 8.283 11842 Z= 0.310 Chirality : 0.043 0.219 1466 Planarity : 0.004 0.040 1404 Dihedral : 9.013 138.154 1194 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.27 % Allowed : 15.99 % Favored : 81.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.91 (0.26), residues: 1070 helix: 2.19 (0.21), residues: 636 sheet: None (None), residues: 0 loop : -1.98 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.015 0.001 TYR B 613 PHE 0.014 0.001 PHE A 235 TRP 0.009 0.001 TRP A 616 HIS 0.003 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.12 ( 8626) covalent geometry : angle 0.62494 / 0.30 (11794) SS BOND : bond 0.00337 / 0.20 ( 6) SS BOND : angle 1.42554 / 0.74 ( 12) hydrogen bonds : bond 0.03826 / 2.50 ( 486) hydrogen bonds : angle 3.73812 / 2.74 ( 1386) Misc. bond : bond 0.00013 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00319 / 0.19 ( 4) link_ALPHA1-4 : angle 0.98680 / 0.55 ( 12) link_BETA1-4 : bond 0.01269 / 0.78 ( 4) link_BETA1-4 : angle 5.48527 / 3.05 ( 12) link_NAG-ASN : bond 0.00259 / 0.15 ( 4) link_NAG-ASN : angle 3.38002 / 2.22 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.294 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8158 (ttm) cc_final: 0.7837 (ttt) REVERT: A 380 LEU cc_start: 0.8630 (mt) cc_final: 0.8390 (mt) REVERT: A 594 LEU cc_start: 0.9047 (tp) cc_final: 0.8824 (tt) REVERT: B 130 GLN cc_start: 0.8017 (tt0) cc_final: 0.7746 (tt0) REVERT: B 380 LEU cc_start: 0.8751 (mt) cc_final: 0.8400 (mt) REVERT: B 594 LEU cc_start: 0.9054 (tp) cc_final: 0.8848 (tt) outliers start: 20 outliers final: 15 residues processed: 163 average time/residue: 0.0754 time to fit residues: 18.2840 Evaluate side-chains 154 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 139 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 537 ASN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 40 optimal weight: 4.9990 chunk 60 optimal weight: 7.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 6.9990 chunk 44 optimal weight: 0.7980 chunk 23 optimal weight: 0.0060 chunk 100 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 92 optimal weight: 0.6980 chunk 7 optimal weight: 0.9980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.135378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.111028 restraints weight = 13716.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.114291 restraints weight = 7777.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.116422 restraints weight = 5533.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117660 restraints weight = 4474.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.118615 restraints weight = 3940.894| |-----------------------------------------------------------------------------| r_work (final): 0.3402 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.3680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8648 Z= 0.121 Angle : 0.663 8.067 11842 Z= 0.311 Chirality : 0.043 0.211 1466 Planarity : 0.004 0.040 1404 Dihedral : 8.940 136.286 1194 Min Nonbonded Distance : 2.242 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.27 % Allowed : 16.44 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1070 helix: 2.18 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -2.00 (0.27), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 445 TYR 0.015 0.001 TYR A 613 PHE 0.014 0.001 PHE A 235 TRP 0.008 0.001 TRP A 616 HIS 0.003 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.12 ( 8626) covalent geometry : angle 0.62976 / 0.30 (11794) SS BOND : bond 0.00381 / 0.23 ( 6) SS BOND : angle 1.43122 / 0.77 ( 12) hydrogen bonds : bond 0.03796 / 2.49 ( 486) hydrogen bonds : angle 3.75020 / 2.74 ( 1386) Misc. bond : bond 0.00013 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00290 / 0.17 ( 4) link_ALPHA1-4 : angle 0.98203 / 0.55 ( 12) link_BETA1-4 : bond 0.01246 / 0.76 ( 4) link_BETA1-4 : angle 5.38800 / 3.00 ( 12) link_NAG-ASN : bond 0.00216 / 0.13 ( 4) link_NAG-ASN : angle 3.39266 / 2.24 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 148 time to evaluate : 0.251 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8126 (ttm) cc_final: 0.7822 (ttt) REVERT: A 380 LEU cc_start: 0.8720 (mt) cc_final: 0.8447 (mt) REVERT: B 130 GLN cc_start: 0.8027 (tt0) cc_final: 0.7784 (tt0) REVERT: B 380 LEU cc_start: 0.8746 (mt) cc_final: 0.8402 (mt) REVERT: B 647 MET cc_start: 0.8372 (ttp) cc_final: 0.8109 (ttp) outliers start: 20 outliers final: 18 residues processed: 157 average time/residue: 0.0746 time to fit residues: 17.3040 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 490 VAL Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 226 THR Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 42 optimal weight: 0.4980 chunk 64 optimal weight: 0.0030 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 8.9990 chunk 105 optimal weight: 0.9980 chunk 82 optimal weight: 1.9990 chunk 78 optimal weight: 0.0070 chunk 26 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 overall best weight: 0.4408 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.137086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.112888 restraints weight = 13570.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.116161 restraints weight = 7745.018| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118334 restraints weight = 5518.827| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.119695 restraints weight = 4447.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.120326 restraints weight = 3886.893| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8190 moved from start: 0.3816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8648 Z= 0.115 Angle : 0.672 10.532 11842 Z= 0.312 Chirality : 0.043 0.205 1466 Planarity : 0.004 0.038 1404 Dihedral : 8.904 135.556 1194 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.15 % Allowed : 17.35 % Favored : 80.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.09 (0.26), residues: 1070 helix: 2.24 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.87 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 313 TYR 0.015 0.001 TYR B 613 PHE 0.018 0.001 PHE B 541 TRP 0.009 0.001 TRP B 616 HIS 0.002 0.000 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00252 / 0.11 ( 8626) covalent geometry : angle 0.64179 / 0.30 (11794) SS BOND : bond 0.00314 / 0.19 ( 6) SS BOND : angle 1.32707 / 0.70 ( 12) hydrogen bonds : bond 0.03593 / 2.36 ( 486) hydrogen bonds : angle 3.72213 / 2.72 ( 1386) Misc. bond : bond 0.00012 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00324 / 0.19 ( 4) link_ALPHA1-4 : angle 0.94721 / 0.55 ( 12) link_BETA1-4 : bond 0.01275 / 0.78 ( 4) link_BETA1-4 : angle 5.20896 / 2.88 ( 12) link_NAG-ASN : bond 0.00316 / 0.18 ( 4) link_NAG-ASN : angle 3.22179 / 2.13 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 154 time to evaluate : 0.310 Fit side-chains revert: symmetry clash REVERT: A 144 MET cc_start: 0.8074 (ttm) cc_final: 0.7800 (ttt) REVERT: A 380 LEU cc_start: 0.8691 (mt) cc_final: 0.8417 (mt) REVERT: B 130 GLN cc_start: 0.7992 (tt0) cc_final: 0.7750 (tt0) REVERT: B 380 LEU cc_start: 0.8700 (mt) cc_final: 0.8320 (mt) REVERT: B 647 MET cc_start: 0.8314 (ttp) cc_final: 0.7972 (ttp) outliers start: 19 outliers final: 16 residues processed: 163 average time/residue: 0.0723 time to fit residues: 17.3214 Evaluate side-chains 160 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 92 optimal weight: 0.9980 chunk 33 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 55 optimal weight: 0.5980 chunk 100 optimal weight: 0.9990 chunk 75 optimal weight: 2.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.135837 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.111471 restraints weight = 13694.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.114736 restraints weight = 7859.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.116854 restraints weight = 5596.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.118173 restraints weight = 4535.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.118912 restraints weight = 3980.436| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8648 Z= 0.130 Angle : 0.694 8.749 11842 Z= 0.322 Chirality : 0.045 0.217 1466 Planarity : 0.004 0.040 1404 Dihedral : 8.857 133.940 1194 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.93 % Allowed : 17.69 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.26), residues: 1070 helix: 2.27 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.79 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 317 TYR 0.015 0.001 TYR A 613 PHE 0.014 0.001 PHE B 541 TRP 0.007 0.001 TRP B 339 HIS 0.003 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8626) covalent geometry : angle 0.66445 / 0.31 (11794) SS BOND : bond 0.00418 / 0.25 ( 6) SS BOND : angle 1.43522 / 0.77 ( 12) hydrogen bonds : bond 0.03751 / 2.47 ( 486) hydrogen bonds : angle 3.77192 / 2.75 ( 1386) Misc. bond : bond 0.00015 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00339 / 0.22 ( 4) link_ALPHA1-4 : angle 1.00901 / 0.57 ( 12) link_BETA1-4 : bond 0.01179 / 0.73 ( 4) link_BETA1-4 : angle 5.20906 / 2.89 ( 12) link_NAG-ASN : bond 0.00170 / 0.10 ( 4) link_NAG-ASN : angle 3.37955 / 2.25 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 145 time to evaluate : 0.307 Fit side-chains REVERT: A 144 MET cc_start: 0.8076 (ttm) cc_final: 0.7813 (ttt) REVERT: A 380 LEU cc_start: 0.8720 (mt) cc_final: 0.8435 (mt) REVERT: B 130 GLN cc_start: 0.8023 (tt0) cc_final: 0.7810 (tt0) REVERT: B 380 LEU cc_start: 0.8730 (mt) cc_final: 0.8355 (mt) REVERT: B 647 MET cc_start: 0.8243 (ttp) cc_final: 0.7986 (ttp) outliers start: 17 outliers final: 16 residues processed: 152 average time/residue: 0.0716 time to fit residues: 16.1635 Evaluate side-chains 158 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 226 THR Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 488 ASP Chi-restraints excluded: chain A residue 538 ILE Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 315 LEU Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 538 ILE Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 596 CYS Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 0.7980 chunk 77 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 94 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 3.9990 chunk 86 optimal weight: 0.5980 chunk 21 optimal weight: 7.9990 chunk 68 optimal weight: 8.9990 chunk 61 optimal weight: 4.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.135194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.110782 restraints weight = 13622.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.113998 restraints weight = 7868.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.116099 restraints weight = 5636.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.117376 restraints weight = 4569.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.118162 restraints weight = 4021.928| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.3899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8648 Z= 0.136 Angle : 0.708 10.270 11842 Z= 0.332 Chirality : 0.045 0.223 1466 Planarity : 0.004 0.039 1404 Dihedral : 8.814 132.478 1194 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.93 % Allowed : 17.91 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.19 (0.26), residues: 1070 helix: 2.27 (0.21), residues: 650 sheet: None (None), residues: 0 loop : -1.74 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 445 TYR 0.016 0.001 TYR A 613 PHE 0.027 0.001 PHE B 541 TRP 0.008 0.001 TRP B 381 HIS 0.002 0.000 HIS B 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.14 ( 8626) covalent geometry : angle 0.67891 / 0.33 (11794) SS BOND : bond 0.00442 / 0.26 ( 6) SS BOND : angle 1.49571 / 0.81 ( 12) hydrogen bonds : bond 0.03895 / 2.57 ( 486) hydrogen bonds : angle 3.82185 / 2.81 ( 1386) Misc. bond : bond 0.00016 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00267 / 0.15 ( 4) link_ALPHA1-4 : angle 0.97160 / 0.55 ( 12) link_BETA1-4 : bond 0.01210 / 0.74 ( 4) link_BETA1-4 : angle 5.17460 / 2.88 ( 12) link_NAG-ASN : bond 0.00146 / 0.09 ( 4) link_NAG-ASN : angle 3.40252 / 2.27 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1360.89 seconds wall clock time: 24 minutes 14.49 seconds (1454.49 seconds total)