Starting phenix.real_space_refine on Fri Sep 11 08:59:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.cif" model { file = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkr_0701/09_2026/6kkr_0701.map" } resolution = 2.9 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= 0.006 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 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: 8416 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: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 2.10, per 1000 atoms: 0.25 Number of scatterers: 8416 At special positions: 0 Unit cell: (75.97, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 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=2.02 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=2.02 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: 0.96 Conformation dependent library (CDL) restraints added in 321.3 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: 52 helices and 4 sheets defined 71.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.753A 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 140 through 176 removed outlier: 7.052A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.721A 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 301 removed outlier: 3.661A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.679A 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 removed outlier: 3.623A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.593A 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: 4.405A 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 removed outlier: 3.545A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.893A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.753A 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 140 through 176 removed outlier: 7.052A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.721A 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 301 removed outlier: 3.661A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.679A 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 removed outlier: 3.623A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.593A 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: 4.405A 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 removed outlier: 3.545A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.577A 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: 3.893A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 650 " --> pdb=" O GLY B 646 " (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 329 496 hydrogen bonds defined for protein. 1416 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: 1.23 Time building geometry restraints manager: 1.21 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: 2320 1.47 - 1.60: 3728 1.60 - 1.73: 0 1.73 - 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 - 2.08: 11149 2.08 - 4.16: 494 4.16 - 6.24: 111 6.24 - 8.32: 27 8.32 - 10.40: 13 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" C PRO B 230 " pdb=" N PRO B 231 " pdb=" CA PRO B 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C PRO A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C ILE A 571 " pdb=" N ALA A 572 " pdb=" CA ALA A 572 " ideal model delta sigma weight residual 122.40 128.23 -5.83 1.45e+00 4.76e-01 1.62e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 4876 34.22 - 68.43: 30 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 A2000 " pdb=" C24 DU0 A2000 " pdb=" C25 DU0 A2000 " pdb=" O23 DU0 A2000 " 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 B2000 " pdb=" C24 DU0 B2000 " pdb=" C25 DU0 B2000 " pdb=" O23 DU0 B2000 " 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 490 " pdb=" C VAL A 490 " pdb=" N SER A 491 " pdb=" CA SER A 491 " ideal model delta harmonic sigma weight residual 180.00 159.21 20.79 0 5.00e+00 4.00e-02 1.73e+01 ... (remaining 4909 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1258 0.083 - 0.167: 194 0.167 - 0.250: 10 0.250 - 0.333: 2 0.333 - 0.417: 2 Chirality restraints: 1466 Sorted by residual: 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 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 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 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 473 " 0.011 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE A 473 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 473 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 473 " -0.000 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 3176 2.91 - 3.46: 9098 3.46 - 4.02: 15205 4.02 - 4.58: 21610 4.58 - 5.14: 31161 Nonbonded interactions: 80250 Sorted by model distance: nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.348 3.040 nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.348 3.040 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 3.040 nonbonded pdb=" O2 GLC I 2 " pdb=" O4 GLC I 2 " model vdw 2.383 3.040 nonbonded pdb=" O GLU A 222 " pdb=" OG1 THR A 226 " model vdw 2.383 3.040 ... (remaining 80245 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: 0.02 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 0.140 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.130 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 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= 0.386 Angle : 1.202 16.269 11842 Z= 0.613 Chirality : 0.061 0.417 1466 Planarity : 0.007 0.063 1404 Dihedral : 11.038 171.079 2926 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.23 % Allowed : 2.38 % Favored : 97.39 % 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: -3.53 (0.20), residues: 1070 helix: -2.09 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 528 TYR 0.027 0.003 TYR B 466 PHE 0.036 0.004 PHE A 473 TRP 0.029 0.003 TRP A 339 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00849 / 0.38 ( 8626) covalent geometry : angle 1.11030 / 0.59 (11794) SS BOND : bond 0.00615 / 0.36 ( 6) SS BOND : angle 2.32835 / 1.16 ( 12) hydrogen bonds : bond 0.20760 / 14.14 ( 496) hydrogen bonds : angle 7.18464 / 5.18 ( 1416) Misc. bond : bond 0.00749 / 0.44 ( 4) link_ALPHA1-4 : bond 0.05558 / 3.29 ( 4) link_ALPHA1-4 : angle 2.30409 / 1.26 ( 12) link_BETA1-4 : bond 0.01151 / 0.71 ( 4) link_BETA1-4 : angle 10.93825 / 6.05 ( 12) link_NAG-ASN : bond 0.00482 / 0.28 ( 4) link_NAG-ASN : angle 9.10026 / 5.93 ( 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 244 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.348 Fit side-chains REVERT: A 400 ASP cc_start: 0.8009 (t0) cc_final: 0.7794 (t0) REVERT: A 405 LYS cc_start: 0.8313 (tttp) cc_final: 0.8077 (tttp) REVERT: A 449 LYS cc_start: 0.8156 (tttp) cc_final: 0.7753 (ttmt) REVERT: A 488 ASP cc_start: 0.8046 (m-30) cc_final: 0.7657 (m-30) REVERT: A 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7093 (mtp85) REVERT: B 400 ASP cc_start: 0.7975 (t0) cc_final: 0.7766 (t0) REVERT: B 405 LYS cc_start: 0.8302 (tttp) cc_final: 0.8064 (tttp) REVERT: B 449 LYS cc_start: 0.8152 (tttp) cc_final: 0.7744 (ttmt) REVERT: B 528 ARG cc_start: 0.7316 (mmt-90) cc_final: 0.7098 (mtp85) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.4995 time to fit residues: 130.6226 Evaluate side-chains 150 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 149 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN A 131 ASN A 347 ASN A 537 ASN A 615 HIS B 130 GLN B 131 ASN B 347 ASN B 537 ASN B 606 ASN B 615 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.126070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.098399 restraints weight = 9825.675| |-----------------------------------------------------------------------------| r_work (start): 0.3045 rms_B_bonded: 2.07 r_work: 0.2918 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8648 Z= 0.144 Angle : 0.818 21.148 11842 Z= 0.361 Chirality : 0.061 1.079 1466 Planarity : 0.005 0.061 1404 Dihedral : 10.101 160.206 1196 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.85 % Allowed : 10.77 % Favored : 85.37 % 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: -1.28 (0.24), residues: 1070 helix: -0.01 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.13 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 440 TYR 0.014 0.001 TYR B 292 PHE 0.010 0.001 PHE B 428 TRP 0.006 0.001 TRP A 501 HIS 0.002 0.001 HIS A 615 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8626) covalent geometry : angle 0.69502 / 0.33 (11794) SS BOND : bond 0.01368 / 0.84 ( 6) SS BOND : angle 1.84396 / 0.96 ( 12) hydrogen bonds : bond 0.04995 / 3.41 ( 496) hydrogen bonds : angle 4.51337 / 3.16 ( 1416) Misc. bond : bond 0.00042 / 0.03 ( 4) link_ALPHA1-4 : bond 0.00191 / 0.12 ( 4) link_ALPHA1-4 : angle 1.56381 / 0.80 ( 12) link_BETA1-4 : bond 0.01491 / 0.91 ( 4) link_BETA1-4 : angle 7.41035 / 3.97 ( 12) link_NAG-ASN : bond 0.01437 / 0.89 ( 4) link_NAG-ASN : angle 11.16826 / 5.99 ( 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 193 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 159 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8441 (m-40) cc_final: 0.8110 (m110) REVERT: A 276 PHE cc_start: 0.7616 (m-10) cc_final: 0.7410 (m-10) REVERT: A 400 ASP cc_start: 0.8707 (t0) cc_final: 0.8396 (t0) REVERT: A 440 ARG cc_start: 0.7636 (mtt-85) cc_final: 0.7402 (mtt-85) REVERT: A 445 ARG cc_start: 0.7834 (mtm110) cc_final: 0.7602 (mtm110) REVERT: A 528 ARG cc_start: 0.8013 (mmt-90) cc_final: 0.7528 (mtp85) REVERT: A 536 ASP cc_start: 0.8173 (OUTLIER) cc_final: 0.7886 (m-30) REVERT: B 274 ASN cc_start: 0.8417 (m-40) cc_final: 0.8075 (m110) REVERT: B 400 ASP cc_start: 0.8678 (t0) cc_final: 0.8361 (t0) REVERT: B 440 ARG cc_start: 0.7645 (mtt-85) cc_final: 0.7420 (mtt-85) REVERT: B 445 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7654 (mtm110) REVERT: B 528 ARG cc_start: 0.8063 (mmt-90) cc_final: 0.7571 (mtp85) REVERT: B 536 ASP cc_start: 0.8183 (OUTLIER) cc_final: 0.7898 (m-30) REVERT: B 612 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8066 (ttmp) outliers start: 34 outliers final: 15 residues processed: 175 average time/residue: 0.5490 time to fit residues: 102.1870 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 : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 536 ASP Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 536 ASP Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 612 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 13 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 49 optimal weight: 4.9990 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 61 optimal weight: 5.9990 chunk 7 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 337 GLN A 606 ASN B 131 ASN B 337 GLN B 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3396 r_free = 0.3396 target = 0.125842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098209 restraints weight = 9663.511| |-----------------------------------------------------------------------------| r_work (start): 0.3104 rms_B_bonded: 2.04 r_work: 0.2977 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2564 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= 0.130 Angle : 0.726 18.778 11842 Z= 0.321 Chirality : 0.052 0.790 1466 Planarity : 0.005 0.051 1404 Dihedral : 9.371 150.160 1194 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 4.99 % Allowed : 10.54 % Favored : 84.47 % 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: -0.19 (0.25), residues: 1070 helix: 0.95 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.82 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 440 TYR 0.011 0.001 TYR A 292 PHE 0.011 0.001 PHE A 428 TRP 0.007 0.001 TRP B 501 HIS 0.001 0.001 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 ( 8626) covalent geometry : angle 0.61735 / 0.29 (11794) SS BOND : bond 0.00103 / 0.06 ( 6) SS BOND : angle 1.93350 / 0.99 ( 12) hydrogen bonds : bond 0.04244 / 2.89 ( 496) hydrogen bonds : angle 4.08611 / 2.83 ( 1416) Misc. bond : bond 0.00015 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00487 / 0.29 ( 4) link_ALPHA1-4 : angle 1.17327 / 0.63 ( 12) link_BETA1-4 : bond 0.01634 / 1.00 ( 4) link_BETA1-4 : angle 6.59131 / 3.55 ( 12) link_NAG-ASN : bond 0.01246 / 0.77 ( 4) link_NAG-ASN : angle 9.84566 / 5.32 ( 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 194 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.301 Fit side-chains REVERT: A 274 ASN cc_start: 0.8439 (m-40) cc_final: 0.8138 (m110) REVERT: A 400 ASP cc_start: 0.8621 (t0) cc_final: 0.8393 (t0) REVERT: A 445 ARG cc_start: 0.7825 (mtm110) cc_final: 0.7575 (mtm110) REVERT: A 496 VAL cc_start: 0.8585 (t) cc_final: 0.8298 (p) REVERT: A 528 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7656 (mtp85) REVERT: B 274 ASN cc_start: 0.8415 (m-40) cc_final: 0.8082 (m110) REVERT: B 400 ASP cc_start: 0.8585 (t0) cc_final: 0.8356 (t0) REVERT: B 445 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7657 (mtm110) REVERT: B 496 VAL cc_start: 0.8564 (t) cc_final: 0.8304 (p) REVERT: B 528 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7655 (mtp85) outliers start: 44 outliers final: 18 residues processed: 175 average time/residue: 0.5136 time to fit residues: 95.9451 Evaluate side-chains 162 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.8980 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 90 optimal weight: 0.0060 chunk 77 optimal weight: 5.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9990 chunk 76 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 overall best weight: 0.9600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN B 377 GLN B 606 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.125091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3024 r_free = 0.3024 target = 0.097227 restraints weight = 9948.932| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.07 r_work: 0.2892 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.2753 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= 0.132 Angle : 0.664 11.161 11842 Z= 0.300 Chirality : 0.042 0.182 1466 Planarity : 0.004 0.046 1404 Dihedral : 9.166 146.914 1194 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.65 % Allowed : 10.88 % Favored : 84.47 % 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: 0.34 (0.26), residues: 1070 helix: 1.39 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.62 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.012 0.001 TYR A 292 PHE 0.012 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.002 0.001 HIS B 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.13 ( 8626) covalent geometry : angle 0.59336 / 0.28 (11794) SS BOND : bond 0.00252 / 0.15 ( 6) SS BOND : angle 2.16024 / 1.01 ( 12) hydrogen bonds : bond 0.03970 / 2.71 ( 496) hydrogen bonds : angle 3.94709 / 2.73 ( 1416) Misc. bond : bond 0.00019 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00408 / 0.25 ( 4) link_ALPHA1-4 : angle 1.35640 / 0.76 ( 12) link_BETA1-4 : bond 0.01549 / 0.94 ( 4) link_BETA1-4 : angle 6.50786 / 3.39 ( 12) link_NAG-ASN : bond 0.00520 / 0.32 ( 4) link_NAG-ASN : angle 6.29061 / 3.61 ( 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 207 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 166 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8372 (m-40) cc_final: 0.8073 (m110) REVERT: A 330 ASP cc_start: 0.7401 (p0) cc_final: 0.7128 (p0) REVERT: A 349 THR cc_start: 0.8465 (OUTLIER) cc_final: 0.8155 (p) REVERT: A 400 ASP cc_start: 0.8706 (t0) cc_final: 0.8455 (t0) REVERT: A 440 ARG cc_start: 0.7650 (mtt-85) cc_final: 0.7371 (mtp85) REVERT: A 488 ASP cc_start: 0.8126 (m-30) cc_final: 0.7454 (m-30) REVERT: A 496 VAL cc_start: 0.8538 (t) cc_final: 0.8268 (p) REVERT: A 528 ARG cc_start: 0.8136 (mmt-90) cc_final: 0.7703 (mtt90) REVERT: B 274 ASN cc_start: 0.8323 (m-40) cc_final: 0.8016 (m110) REVERT: B 349 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8129 (p) REVERT: B 400 ASP cc_start: 0.8675 (t0) cc_final: 0.8418 (t0) REVERT: B 443 ASP cc_start: 0.8018 (m-30) cc_final: 0.7178 (t0) REVERT: B 445 ARG cc_start: 0.7967 (mtm110) cc_final: 0.7602 (mtm110) REVERT: B 496 VAL cc_start: 0.8516 (t) cc_final: 0.8281 (p) REVERT: B 528 ARG cc_start: 0.8148 (mmt-90) cc_final: 0.7688 (mtp85) outliers start: 41 outliers final: 21 residues processed: 186 average time/residue: 0.5498 time to fit residues: 109.0010 Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 151 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 521 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 0.8980 chunk 46 optimal weight: 0.6980 chunk 10 optimal weight: 0.7980 chunk 78 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 79 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 98 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.123432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095539 restraints weight = 9906.807| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 2.06 r_work: 0.2919 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2781 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2781 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 moved from start: 0.2886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8648 Z= 0.142 Angle : 0.641 8.946 11842 Z= 0.297 Chirality : 0.042 0.188 1466 Planarity : 0.004 0.044 1404 Dihedral : 9.046 144.226 1194 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.10 % Allowed : 11.34 % Favored : 83.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.26), residues: 1070 helix: 1.59 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.49 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 191 TYR 0.013 0.001 TYR A 613 PHE 0.012 0.001 PHE B 428 TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.14 ( 8626) covalent geometry : angle 0.58716 / 0.28 (11794) SS BOND : bond 0.00296 / 0.17 ( 6) SS BOND : angle 2.27314 / 1.07 ( 12) hydrogen bonds : bond 0.04121 / 2.80 ( 496) hydrogen bonds : angle 3.86314 / 2.67 ( 1416) Misc. bond : bond 0.00032 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00398 / 0.24 ( 4) link_ALPHA1-4 : angle 1.32422 / 0.75 ( 12) link_BETA1-4 : bond 0.00953 / 0.58 ( 4) link_BETA1-4 : angle 5.71878 / 2.95 ( 12) link_NAG-ASN : bond 0.00197 / 0.12 ( 4) link_NAG-ASN : angle 5.23863 / 3.25 ( 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 198 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 153 time to evaluate : 0.331 Fit side-chains REVERT: A 274 ASN cc_start: 0.8411 (m-40) cc_final: 0.8108 (m110) REVERT: A 301 ASP cc_start: 0.7844 (t0) cc_final: 0.7508 (t0) REVERT: A 349 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8166 (p) REVERT: A 440 ARG cc_start: 0.7467 (mtt-85) cc_final: 0.7185 (mtp85) REVERT: A 496 VAL cc_start: 0.8600 (t) cc_final: 0.8365 (p) REVERT: A 528 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7773 (mtt90) REVERT: B 274 ASN cc_start: 0.8355 (m-40) cc_final: 0.8050 (m110) REVERT: B 301 ASP cc_start: 0.7795 (t0) cc_final: 0.7478 (t0) REVERT: B 349 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 440 ARG cc_start: 0.7785 (mtp85) cc_final: 0.7520 (mtp180) REVERT: B 496 VAL cc_start: 0.8593 (t) cc_final: 0.8367 (p) REVERT: B 528 ARG cc_start: 0.8190 (mmt-90) cc_final: 0.7736 (mtp85) outliers start: 45 outliers final: 22 residues processed: 176 average time/residue: 0.5365 time to fit residues: 100.5997 Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 492 ARG 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 38 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 87 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 99 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096285 restraints weight = 9826.372| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.05 r_work: 0.2939 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.3041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8648 Z= 0.134 Angle : 0.750 20.359 11842 Z= 0.327 Chirality : 0.056 0.937 1466 Planarity : 0.004 0.043 1404 Dihedral : 9.049 145.225 1194 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 4.76 % Allowed : 14.29 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.83 (0.26), residues: 1070 helix: 1.78 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.43 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.012 0.001 TYR A 292 PHE 0.010 0.001 PHE B 428 TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.13 ( 8626) covalent geometry : angle 0.63743 / 0.30 (11794) SS BOND : bond 0.00298 / 0.19 ( 6) SS BOND : angle 2.13611 / 1.07 ( 12) hydrogen bonds : bond 0.03938 / 2.68 ( 496) hydrogen bonds : angle 3.82482 / 2.64 ( 1416) Misc. bond : bond 0.00027 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00391 / 0.23 ( 4) link_ALPHA1-4 : angle 1.32566 / 0.77 ( 12) link_BETA1-4 : bond 0.00905 / 0.55 ( 4) link_BETA1-4 : angle 6.10708 / 3.09 ( 12) link_NAG-ASN : bond 0.00554 / 0.34 ( 4) link_NAG-ASN : angle 10.62166 / 5.33 ( 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 192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 150 time to evaluate : 0.244 Fit side-chains REVERT: A 274 ASN cc_start: 0.8389 (m-40) cc_final: 0.8104 (m110) REVERT: A 301 ASP cc_start: 0.7848 (t0) cc_final: 0.7508 (t0) REVERT: A 349 THR cc_start: 0.8428 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 484 ASP cc_start: 0.8014 (OUTLIER) cc_final: 0.7627 (t0) REVERT: A 496 VAL cc_start: 0.8609 (t) cc_final: 0.8377 (p) REVERT: A 528 ARG cc_start: 0.8172 (mmt-90) cc_final: 0.7796 (mtt180) REVERT: B 274 ASN cc_start: 0.8365 (m-40) cc_final: 0.8075 (m110) REVERT: B 301 ASP cc_start: 0.7808 (t0) cc_final: 0.7491 (t0) REVERT: B 349 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 440 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7497 (mtp180) REVERT: B 445 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7695 (mtm110) REVERT: B 484 ASP cc_start: 0.7975 (OUTLIER) cc_final: 0.7609 (t0) REVERT: B 496 VAL cc_start: 0.8601 (t) cc_final: 0.8378 (p) REVERT: B 528 ARG cc_start: 0.8184 (mmt-90) cc_final: 0.7726 (mtp85) outliers start: 42 outliers final: 23 residues processed: 173 average time/residue: 0.5609 time to fit residues: 103.3472 Evaluate side-chains 177 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 150 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 78 optimal weight: 0.5980 chunk 73 optimal weight: 7.9990 chunk 27 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 0.0970 chunk 38 optimal weight: 0.0970 chunk 23 optimal weight: 2.9990 overall best weight: 0.9578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN A 377 GLN A 606 ASN B 131 ASN B 319 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.124063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.096366 restraints weight = 9954.838| |-----------------------------------------------------------------------------| r_work (start): 0.3087 rms_B_bonded: 2.06 r_work: 0.2960 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8480 moved from start: 0.3110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8648 Z= 0.146 Angle : 0.719 12.834 11842 Z= 0.326 Chirality : 0.045 0.297 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.092 145.311 1194 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 4.31 % Allowed : 16.21 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.04 (0.26), residues: 1070 helix: 1.94 (0.21), residues: 646 sheet: None (None), residues: 0 loop : -1.35 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 191 TYR 0.012 0.001 TYR A 292 PHE 0.010 0.001 PHE B 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8626) covalent geometry : angle 0.65892 / 0.31 (11794) SS BOND : bond 0.00216 / 0.13 ( 6) SS BOND : angle 2.23420 / 0.99 ( 12) hydrogen bonds : bond 0.03854 / 2.63 ( 496) hydrogen bonds : angle 3.78971 / 2.62 ( 1416) Misc. bond : bond 0.00026 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00401 / 0.24 ( 4) link_ALPHA1-4 : angle 1.31301 / 0.76 ( 12) link_BETA1-4 : bond 0.03072 / 1.89 ( 4) link_BETA1-4 : angle 4.14812 / 2.30 ( 12) link_NAG-ASN : bond 0.00470 / 0.29 ( 4) link_NAG-ASN : angle 7.72133 / 4.78 ( 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 195 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 157 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8399 (m-40) cc_final: 0.8096 (m110) REVERT: A 301 ASP cc_start: 0.7818 (t0) cc_final: 0.7471 (t0) REVERT: A 349 THR cc_start: 0.8424 (OUTLIER) cc_final: 0.8092 (p) REVERT: A 440 ARG cc_start: 0.7601 (mtp85) cc_final: 0.7234 (mtp180) REVERT: A 484 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7625 (t0) REVERT: A 496 VAL cc_start: 0.8594 (t) cc_final: 0.8383 (p) REVERT: A 528 ARG cc_start: 0.8171 (mmt-90) cc_final: 0.7804 (mtt180) REVERT: B 274 ASN cc_start: 0.8370 (m-40) cc_final: 0.8073 (m110) REVERT: B 301 ASP cc_start: 0.7806 (t0) cc_final: 0.7465 (t0) REVERT: B 349 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8064 (p) REVERT: B 440 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7481 (mtp180) REVERT: B 445 ARG cc_start: 0.8030 (mtm110) cc_final: 0.7688 (mtm110) REVERT: B 484 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7594 (t0) REVERT: B 496 VAL cc_start: 0.8591 (t) cc_final: 0.8388 (p) REVERT: B 528 ARG cc_start: 0.8169 (mmt-90) cc_final: 0.7812 (mtt180) outliers start: 38 outliers final: 28 residues processed: 180 average time/residue: 0.5401 time to fit residues: 103.8753 Evaluate side-chains 182 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 150 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 23 optimal weight: 2.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN A 377 GLN B 131 ASN B 319 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3359 r_free = 0.3359 target = 0.123047 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.095422 restraints weight = 9844.478| |-----------------------------------------------------------------------------| r_work (start): 0.2993 rms_B_bonded: 2.04 r_work: 0.2861 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2721 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 8648 Z= 0.151 Angle : 0.690 11.870 11842 Z= 0.321 Chirality : 0.045 0.288 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.099 145.228 1194 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.76 % Allowed : 15.87 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.07 (0.26), residues: 1070 helix: 1.81 (0.20), residues: 660 sheet: 2.67 (1.33), residues: 20 loop : -1.41 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.012 0.001 TYR B 292 PHE 0.012 0.001 PHE B 428 TRP 0.006 0.001 TRP A 556 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 8626) covalent geometry : angle 0.63002 / 0.31 (11794) SS BOND : bond 0.00424 / 0.27 ( 6) SS BOND : angle 2.44829 / 1.20 ( 12) hydrogen bonds : bond 0.04061 / 2.76 ( 496) hydrogen bonds : angle 3.83333 / 2.64 ( 1416) Misc. bond : bond 0.00031 / 0.02 ( 4) link_ALPHA1-4 : bond 0.00394 / 0.23 ( 4) link_ALPHA1-4 : angle 1.34208 / 0.77 ( 12) link_BETA1-4 : bond 0.01136 / 0.70 ( 4) link_BETA1-4 : angle 4.38993 / 2.40 ( 12) link_NAG-ASN : bond 0.00153 / 0.09 ( 4) link_NAG-ASN : angle 7.24694 / 4.61 ( 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 195 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 153 time to evaluate : 0.311 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8320 (m-40) cc_final: 0.8009 (m110) REVERT: A 301 ASP cc_start: 0.7795 (t0) cc_final: 0.7424 (t0) REVERT: A 349 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8080 (p) REVERT: A 440 ARG cc_start: 0.7582 (mtp85) cc_final: 0.7273 (mtp180) REVERT: A 484 ASP cc_start: 0.8022 (OUTLIER) cc_final: 0.7619 (t0) REVERT: A 496 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8329 (p) REVERT: A 521 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8159 (mp10) REVERT: A 528 ARG cc_start: 0.8113 (mmt-90) cc_final: 0.7719 (mtt180) REVERT: B 274 ASN cc_start: 0.8299 (m-40) cc_final: 0.7978 (m110) REVERT: B 301 ASP cc_start: 0.7779 (t0) cc_final: 0.7418 (t0) REVERT: B 349 THR cc_start: 0.8389 (OUTLIER) cc_final: 0.8065 (p) REVERT: B 440 ARG cc_start: 0.7688 (mtp85) cc_final: 0.7433 (mtp180) REVERT: B 445 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7712 (mtm110) REVERT: B 484 ASP cc_start: 0.8036 (OUTLIER) cc_final: 0.7667 (t0) REVERT: B 521 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8069 (mp10) REVERT: B 528 ARG cc_start: 0.8122 (mmt-90) cc_final: 0.7719 (mtt180) outliers start: 42 outliers final: 26 residues processed: 176 average time/residue: 0.5736 time to fit residues: 107.4078 Evaluate side-chains 183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 150 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 521 GLN 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 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 78 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.0070 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 0.9990 chunk 69 optimal weight: 0.8980 chunk 94 optimal weight: 2.9990 chunk 101 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN B 131 ASN B 319 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.125416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097765 restraints weight = 9829.837| |-----------------------------------------------------------------------------| r_work (start): 0.3031 rms_B_bonded: 2.04 r_work: 0.2902 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3300 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 : 0.654 11.147 11842 Z= 0.303 Chirality : 0.043 0.236 1466 Planarity : 0.004 0.041 1404 Dihedral : 8.998 144.495 1194 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.63 % Allowed : 16.89 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.34 (0.26), residues: 1070 helix: 2.08 (0.21), residues: 658 sheet: 2.77 (1.33), residues: 20 loop : -1.39 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 191 TYR 0.011 0.001 TYR A 292 PHE 0.008 0.001 PHE A 211 TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00266 / 0.12 ( 8626) covalent geometry : angle 0.59287 / 0.29 (11794) SS BOND : bond 0.00187 / 0.11 ( 6) SS BOND : angle 1.94392 / 0.95 ( 12) hydrogen bonds : bond 0.03631 / 2.48 ( 496) hydrogen bonds : angle 3.74934 / 2.59 ( 1416) Misc. bond : bond 0.00015 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00404 / 0.24 ( 4) link_ALPHA1-4 : angle 1.27177 / 0.76 ( 12) link_BETA1-4 : bond 0.01283 / 0.79 ( 4) link_BETA1-4 : angle 4.34488 / 2.36 ( 12) link_NAG-ASN : bond 0.00284 / 0.17 ( 4) link_NAG-ASN : angle 7.19777 / 4.43 ( 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 183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 151 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8311 (m-40) cc_final: 0.8027 (m110) REVERT: A 301 ASP cc_start: 0.7747 (t0) cc_final: 0.7386 (t0) REVERT: A 349 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8102 (p) REVERT: A 484 ASP cc_start: 0.7938 (OUTLIER) cc_final: 0.7527 (t0) REVERT: A 496 VAL cc_start: 0.8529 (t) cc_final: 0.8326 (p) REVERT: A 521 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: A 528 ARG cc_start: 0.8092 (mmt-90) cc_final: 0.7706 (mtt180) REVERT: B 274 ASN cc_start: 0.8294 (m-40) cc_final: 0.8006 (m110) REVERT: B 301 ASP cc_start: 0.7734 (t0) cc_final: 0.7383 (t0) REVERT: B 349 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8087 (p) REVERT: B 440 ARG cc_start: 0.7521 (mtp85) cc_final: 0.7289 (mtp180) REVERT: B 445 ARG cc_start: 0.7972 (mtm110) cc_final: 0.7614 (mtm110) REVERT: B 484 ASP cc_start: 0.7924 (OUTLIER) cc_final: 0.7522 (t0) REVERT: B 521 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.8077 (mp10) REVERT: B 528 ARG cc_start: 0.8084 (mmt-90) cc_final: 0.7694 (mtt180) outliers start: 32 outliers final: 24 residues processed: 171 average time/residue: 0.5601 time to fit residues: 101.9633 Evaluate side-chains 174 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 144 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 521 GLN 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 51 optimal weight: 0.6980 chunk 49 optimal weight: 0.9990 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 42 optimal weight: 9.9990 chunk 25 optimal weight: 0.0670 chunk 102 optimal weight: 0.0870 chunk 18 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 chunk 32 optimal weight: 0.0470 chunk 89 optimal weight: 0.8980 overall best weight: 0.3594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 131 ASN A 319 GLN B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.127010 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.099435 restraints weight = 9883.868| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.04 r_work: 0.2975 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8648 Z= 0.117 Angle : 0.643 10.684 11842 Z= 0.298 Chirality : 0.042 0.203 1466 Planarity : 0.004 0.041 1404 Dihedral : 8.898 142.435 1194 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 3.40 % Allowed : 17.35 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.53 (0.26), residues: 1070 helix: 2.25 (0.20), residues: 658 sheet: 2.66 (1.29), residues: 20 loop : -1.33 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 191 TYR 0.013 0.001 TYR B 216 PHE 0.008 0.001 PHE A 133 TRP 0.006 0.001 TRP B 501 HIS 0.000 0.000 HIS B 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00255 / 0.12 ( 8626) covalent geometry : angle 0.58256 / 0.28 (11794) SS BOND : bond 0.00211 / 0.13 ( 6) SS BOND : angle 2.27122 / 1.08 ( 12) hydrogen bonds : bond 0.03436 / 2.34 ( 496) hydrogen bonds : angle 3.70194 / 2.55 ( 1416) Misc. bond : bond 0.00012 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00408 / 0.24 ( 4) link_ALPHA1-4 : angle 1.25755 / 0.76 ( 12) link_BETA1-4 : bond 0.01185 / 0.71 ( 4) link_BETA1-4 : angle 4.22537 / 2.30 ( 12) link_NAG-ASN : bond 0.00319 / 0.18 ( 4) link_NAG-ASN : angle 7.09116 / 4.35 ( 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 179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 149 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8364 (m-40) cc_final: 0.8056 (m110) REVERT: A 301 ASP cc_start: 0.7806 (t0) cc_final: 0.7395 (t0) REVERT: A 349 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.8013 (p) REVERT: A 484 ASP cc_start: 0.7905 (OUTLIER) cc_final: 0.7521 (t0) REVERT: A 521 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.8207 (mp10) REVERT: A 528 ARG cc_start: 0.8123 (mmt-90) cc_final: 0.7756 (mtt180) REVERT: B 274 ASN cc_start: 0.8339 (m-40) cc_final: 0.8038 (m110) REVERT: B 301 ASP cc_start: 0.7804 (t0) cc_final: 0.7444 (t0) REVERT: B 349 THR cc_start: 0.8369 (OUTLIER) cc_final: 0.8075 (p) REVERT: B 440 ARG cc_start: 0.7501 (mtp85) cc_final: 0.7276 (mtp180) REVERT: B 445 ARG cc_start: 0.7982 (mtm110) cc_final: 0.7635 (mtm110) REVERT: B 484 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7462 (t0) REVERT: B 521 GLN cc_start: 0.8493 (OUTLIER) cc_final: 0.8104 (mp10) REVERT: B 528 ARG cc_start: 0.8134 (mmt-90) cc_final: 0.7759 (mtt180) outliers start: 30 outliers final: 19 residues processed: 168 average time/residue: 0.5757 time to fit residues: 103.0665 Evaluate side-chains 166 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 141 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 361 ASN Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 361 ASN Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 521 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 30 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 80 optimal weight: 0.8980 chunk 11 optimal weight: 0.0670 chunk 77 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.7518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 319 GLN B 319 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.098282 restraints weight = 9866.547| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.03 r_work: 0.2995 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.3460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8648 Z= 0.122 Angle : 0.645 10.129 11842 Z= 0.299 Chirality : 0.042 0.189 1466 Planarity : 0.004 0.041 1404 Dihedral : 8.852 141.524 1194 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.95 % Allowed : 18.14 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % 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: 1.56 (0.26), residues: 1070 helix: 2.24 (0.20), residues: 660 sheet: 2.48 (1.25), residues: 20 loop : -1.27 (0.30), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.012 0.001 TYR A 292 PHE 0.010 0.001 PHE A 428 TRP 0.006 0.001 TRP A 556 HIS 0.001 0.000 HIS A 547 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8626) covalent geometry : angle 0.58848 / 0.29 (11794) SS BOND : bond 0.00245 / 0.15 ( 6) SS BOND : angle 2.62322 / 1.28 ( 12) hydrogen bonds : bond 0.03551 / 2.42 ( 496) hydrogen bonds : angle 3.69466 / 2.55 ( 1416) Misc. bond : bond 0.00020 / 0.01 ( 4) link_ALPHA1-4 : bond 0.00416 / 0.25 ( 4) link_ALPHA1-4 : angle 1.23201 / 0.72 ( 12) link_BETA1-4 : bond 0.01128 / 0.69 ( 4) link_BETA1-4 : angle 3.97509 / 2.17 ( 12) link_NAG-ASN : bond 0.00297 / 0.17 ( 4) link_NAG-ASN : angle 6.77011 / 4.20 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2956.68 seconds wall clock time: 51 minutes 7.84 seconds (3067.84 seconds total)