Starting phenix.real_space_refine on Sat Jul 26 17:59:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_0701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_0701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_0701.map" model { file = "/net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_0701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkr_0701/07_2025/6kkr_0701.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 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: 5.84, per 1000 atoms: 0.69 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: 2.52 Conformation dependent library (CDL) restraints added in 1.1 seconds 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: 0.77 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: 2.29 Time building geometry restraints manager: 2.91 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 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+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 1.402 1.485 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11129 2.08 - 4.16: 506 4.16 - 6.24: 123 6.24 - 8.32: 21 8.32 - 10.40: 15 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: 5238 34.22 - 68.43: 52 68.43 - 102.65: 42 102.65 - 136.86: 32 136.86 - 171.08: 2 Dihedral angle restraints: 5366 sinusoidal: 2284 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=" O2 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sinusoidal sigma weight residual 60.18 -167.16 -132.66 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1252 0.083 - 0.167: 198 0.167 - 0.250: 12 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: 0.00 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: 0.740 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: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 23.410 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.040 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:11.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 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 0.088 8648 Z= 0.387 Angle : 1.213 16.269 11842 Z= 0.616 Chirality : 0.061 0.417 1466 Planarity : 0.007 0.063 1404 Dihedral : 18.504 171.079 3380 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.23 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.029 0.003 TRP A 339 HIS 0.003 0.001 HIS B 394 PHE 0.036 0.004 PHE A 473 TYR 0.027 0.003 TYR B 466 ARG 0.006 0.001 ARG B 528 Details of bonding type rmsd link_NAG-ASN : bond 0.00482 ( 4) link_NAG-ASN : angle 9.10026 ( 12) link_ALPHA1-4 : bond 0.05558 ( 4) link_ALPHA1-4 : angle 2.30409 ( 12) link_BETA1-4 : bond 0.01151 ( 4) link_BETA1-4 : angle 10.93825 ( 12) hydrogen bonds : bond 0.20760 ( 496) hydrogen bonds : angle 7.18464 ( 1416) SS BOND : bond 0.00615 ( 6) SS BOND : angle 2.32835 ( 12) covalent geometry : bond 0.00851 ( 8626) covalent geometry : angle 1.12315 (11794) Misc. bond : bond 0.00749 ( 4) *********************** 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 : 0.815 Fit side-chains REVERT: A 400 ASP cc_start: 0.8009 (t0) cc_final: 0.7793 (t0) REVERT: A 405 LYS cc_start: 0.8314 (tttp) cc_final: 0.8078 (tttp) REVERT: A 449 LYS cc_start: 0.8156 (tttp) cc_final: 0.7754 (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: 0.7765 (t0) REVERT: B 405 LYS cc_start: 0.8302 (tttp) cc_final: 0.8065 (tttp) REVERT: B 449 LYS cc_start: 0.8152 (tttp) cc_final: 0.7744 (ttmt) REVERT: B 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7098 (mtp85) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 1.0477 time to fit residues: 273.5134 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 : 0.843 ------------------------------------------------------------------------------- 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 89 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3395 r_free = 0.3395 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097870 restraints weight = 9749.166| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.04 r_work: 0.2905 rms_B_bonded: 2.48 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: 0.8139 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8648 Z= 0.152 Angle : 0.885 24.761 11842 Z= 0.377 Chirality : 0.058 1.003 1466 Planarity : 0.005 0.058 1404 Dihedral : 15.827 145.443 1650 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.74 % Allowed : 10.88 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1070 helix: 0.02 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS A 394 PHE 0.011 0.002 PHE B 427 TYR 0.015 0.002 TYR B 292 ARG 0.004 0.001 ARG B 317 Details of bonding type rmsd link_NAG-ASN : bond 0.01219 ( 4) link_NAG-ASN : angle 12.97993 ( 12) link_ALPHA1-4 : bond 0.00915 ( 4) link_ALPHA1-4 : angle 2.09998 ( 12) link_BETA1-4 : bond 0.00929 ( 4) link_BETA1-4 : angle 7.52207 ( 12) hydrogen bonds : bond 0.04911 ( 496) hydrogen bonds : angle 4.45142 ( 1416) SS BOND : bond 0.00369 ( 6) SS BOND : angle 1.81511 ( 12) covalent geometry : bond 0.00350 ( 8626) covalent geometry : angle 0.74144 (11794) Misc. bond : bond 0.00058 ( 4) *********************** 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 192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 0.887 Fit side-chains REVERT: A 274 ASN cc_start: 0.8422 (m-40) cc_final: 0.8095 (m110) REVERT: A 400 ASP cc_start: 0.8705 (t0) cc_final: 0.8402 (t0) REVERT: A 528 ARG cc_start: 0.8090 (mmt-90) cc_final: 0.7617 (mtp85) REVERT: A 612 LYS cc_start: 0.8527 (OUTLIER) cc_final: 0.8104 (ttmp) REVERT: B 274 ASN cc_start: 0.8400 (m-40) cc_final: 0.8060 (m110) REVERT: B 400 ASP cc_start: 0.8676 (t0) cc_final: 0.8369 (t0) REVERT: B 445 ARG cc_start: 0.8024 (mtm110) cc_final: 0.7677 (mtm110) REVERT: B 528 ARG cc_start: 0.8037 (mmt-90) cc_final: 0.7556 (mtp85) REVERT: B 612 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8087 (ttmp) outliers start: 33 outliers final: 15 residues processed: 174 average time/residue: 1.2177 time to fit residues: 225.0007 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.804 ------------------------------------------------------------------------------- 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 600 THR Chi-restraints excluded: chain A residue 612 LYS 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 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 20 optimal weight: 8.9990 chunk 21 optimal weight: 10.0000 chunk 28 optimal weight: 0.0970 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.6980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 606 ASN B 131 ASN B 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.098115 restraints weight = 9922.643| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.08 r_work: 0.2982 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2617 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= 0.125 Angle : 0.674 12.336 11842 Z= 0.305 Chirality : 0.041 0.176 1466 Planarity : 0.004 0.049 1404 Dihedral : 12.726 145.838 1648 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.65 % Allowed : 10.43 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.25), residues: 1070 helix: 0.95 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 PHE 0.010 0.001 PHE B 276 TYR 0.011 0.001 TYR A 292 ARG 0.003 0.000 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00986 ( 4) link_NAG-ASN : angle 5.05304 ( 12) link_ALPHA1-4 : bond 0.01010 ( 4) link_ALPHA1-4 : angle 1.76090 ( 12) link_BETA1-4 : bond 0.01348 ( 4) link_BETA1-4 : angle 6.86580 ( 12) hydrogen bonds : bond 0.04151 ( 496) hydrogen bonds : angle 4.08368 ( 1416) SS BOND : bond 0.00582 ( 6) SS BOND : angle 1.74981 ( 12) covalent geometry : bond 0.00277 ( 8626) covalent geometry : angle 0.61272 (11794) Misc. bond : bond 0.00015 ( 4) *********************** 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 199 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 158 time to evaluate : 0.898 Fit side-chains REVERT: A 274 ASN cc_start: 0.8429 (m-40) cc_final: 0.8119 (m110) REVERT: A 400 ASP cc_start: 0.8536 (t0) cc_final: 0.8328 (t0) REVERT: A 488 ASP cc_start: 0.8174 (m-30) cc_final: 0.7554 (m-30) REVERT: A 496 VAL cc_start: 0.8529 (t) cc_final: 0.8250 (p) REVERT: A 528 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7676 (mtp85) REVERT: B 274 ASN cc_start: 0.8405 (m-40) cc_final: 0.8091 (m110) REVERT: B 400 ASP cc_start: 0.8490 (t0) cc_final: 0.8282 (t0) REVERT: B 445 ARG cc_start: 0.8033 (mtm110) cc_final: 0.7661 (mtm110) REVERT: B 496 VAL cc_start: 0.8522 (t) cc_final: 0.8251 (p) REVERT: B 528 ARG cc_start: 0.8137 (mmt-90) cc_final: 0.7671 (mtp85) outliers start: 41 outliers final: 17 residues processed: 180 average time/residue: 1.0887 time to fit residues: 209.2433 Evaluate side-chains 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 185 SER 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 476 CYS Chi-restraints excluded: chain B residue 492 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 93 optimal weight: 0.8980 chunk 92 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 44 optimal weight: 0.0570 chunk 12 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 43 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 64 optimal weight: 0.0980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.127883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.099806 restraints weight = 9843.344| |-----------------------------------------------------------------------------| r_work (start): 0.3125 rms_B_bonded: 2.06 r_work: 0.2999 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 8648 Z= 0.114 Angle : 0.629 11.084 11842 Z= 0.286 Chirality : 0.042 0.178 1466 Planarity : 0.004 0.045 1404 Dihedral : 10.763 142.027 1648 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 3.97 % Allowed : 11.34 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.26), residues: 1070 helix: 1.54 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.55 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS B 394 PHE 0.011 0.001 PHE B 428 TYR 0.011 0.001 TYR A 216 ARG 0.004 0.000 ARG B 440 Details of bonding type rmsd link_NAG-ASN : bond 0.00387 ( 4) link_NAG-ASN : angle 3.97542 ( 12) link_ALPHA1-4 : bond 0.01380 ( 4) link_ALPHA1-4 : angle 2.08156 ( 12) link_BETA1-4 : bond 0.01441 ( 4) link_BETA1-4 : angle 6.66412 ( 12) hydrogen bonds : bond 0.03580 ( 496) hydrogen bonds : angle 3.85244 ( 1416) SS BOND : bond 0.00084 ( 6) SS BOND : angle 1.90531 ( 12) covalent geometry : bond 0.00241 ( 8626) covalent geometry : angle 0.57254 (11794) Misc. bond : bond 0.00010 ( 4) *********************** 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 189 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.814 Fit side-chains REVERT: A 274 ASN cc_start: 0.8409 (m-40) cc_final: 0.8125 (m110) REVERT: A 349 THR cc_start: 0.8501 (OUTLIER) cc_final: 0.8199 (p) REVERT: A 400 ASP cc_start: 0.8545 (t0) cc_final: 0.8339 (t0) REVERT: A 440 ARG cc_start: 0.7667 (mtt-85) cc_final: 0.7363 (mtp85) REVERT: A 496 VAL cc_start: 0.8577 (t) cc_final: 0.8330 (p) REVERT: A 528 ARG cc_start: 0.8188 (mmt-90) cc_final: 0.7768 (mtt90) REVERT: B 274 ASN cc_start: 0.8382 (m-40) cc_final: 0.8103 (m110) REVERT: B 349 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8120 (p) REVERT: B 440 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7374 (mtp85) REVERT: B 445 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7654 (mtm110) REVERT: B 496 VAL cc_start: 0.8567 (t) cc_final: 0.8334 (p) REVERT: B 528 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7778 (mtt90) outliers start: 35 outliers final: 17 residues processed: 169 average time/residue: 1.2036 time to fit residues: 216.0040 Evaluate side-chains 165 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 146 time to evaluate : 0.929 ------------------------------------------------------------------------------- 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 349 THR Chi-restraints excluded: chain A residue 408 LEU 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 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 300 PHE Chi-restraints excluded: chain B residue 349 THR 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 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 101 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.122247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.094232 restraints weight = 9826.070| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 2.06 r_work: 0.2845 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2704 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 8648 Z= 0.178 Angle : 0.688 10.693 11842 Z= 0.316 Chirality : 0.044 0.178 1466 Planarity : 0.004 0.045 1404 Dihedral : 10.014 144.139 1648 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.33 % Allowed : 11.34 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.25), residues: 1070 helix: 1.55 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.44 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 381 HIS 0.002 0.001 HIS A 394 PHE 0.015 0.002 PHE B 428 TYR 0.015 0.002 TYR B 411 ARG 0.007 0.000 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00095 ( 4) link_NAG-ASN : angle 4.55208 ( 12) link_ALPHA1-4 : bond 0.01430 ( 4) link_ALPHA1-4 : angle 2.00039 ( 12) link_BETA1-4 : bond 0.01318 ( 4) link_BETA1-4 : angle 6.46168 ( 12) hydrogen bonds : bond 0.04409 ( 496) hydrogen bonds : angle 3.92767 ( 1416) SS BOND : bond 0.00151 ( 6) SS BOND : angle 2.70000 ( 12) covalent geometry : bond 0.00445 ( 8626) covalent geometry : angle 0.63232 (11794) Misc. bond : bond 0.00030 ( 4) *********************** 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: 47 poor density : 151 time to evaluate : 0.908 Fit side-chains REVERT: A 274 ASN cc_start: 0.8372 (m-40) cc_final: 0.8072 (m110) REVERT: A 301 ASP cc_start: 0.7832 (t0) cc_final: 0.7472 (t0) REVERT: A 349 THR cc_start: 0.8472 (OUTLIER) cc_final: 0.8167 (p) REVERT: A 440 ARG cc_start: 0.7701 (mtt-85) cc_final: 0.7358 (mtp180) REVERT: A 496 VAL cc_start: 0.8551 (t) cc_final: 0.8316 (p) REVERT: A 528 ARG cc_start: 0.8165 (mmt-90) cc_final: 0.7701 (mtp85) REVERT: B 274 ASN cc_start: 0.8351 (m-40) cc_final: 0.8044 (m110) REVERT: B 301 ASP cc_start: 0.7806 (t0) cc_final: 0.7472 (t0) REVERT: B 349 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8140 (p) REVERT: B 405 LYS cc_start: 0.8007 (tttp) cc_final: 0.7806 (tttp) REVERT: B 440 ARG cc_start: 0.7717 (mtt-85) cc_final: 0.7414 (mtp180) REVERT: B 484 ASP cc_start: 0.8042 (OUTLIER) cc_final: 0.7694 (t0) REVERT: B 496 VAL cc_start: 0.8555 (t) cc_final: 0.8328 (p) REVERT: B 528 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7722 (mtp85) outliers start: 47 outliers final: 24 residues processed: 175 average time/residue: 1.2088 time to fit residues: 225.0199 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 : 0.931 ------------------------------------------------------------------------------- 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 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 364 GLU 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 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 364 GLU 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 377 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 = 0.3370 r_free = 0.3370 target = 0.123668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.095757 restraints weight = 9733.489| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 2.05 r_work: 0.2955 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3140 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= 0.138 Angle : 0.650 10.433 11842 Z= 0.298 Chirality : 0.042 0.173 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.299 144.640 1648 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 5.44 % Allowed : 13.49 % Favored : 81.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1070 helix: 1.84 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.36 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS B 394 PHE 0.010 0.001 PHE B 428 TYR 0.012 0.001 TYR A 292 ARG 0.006 0.000 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00191 ( 4) link_NAG-ASN : angle 4.25770 ( 12) link_ALPHA1-4 : bond 0.01494 ( 4) link_ALPHA1-4 : angle 2.02885 ( 12) link_BETA1-4 : bond 0.01440 ( 4) link_BETA1-4 : angle 6.28210 ( 12) hydrogen bonds : bond 0.03947 ( 496) hydrogen bonds : angle 3.82299 ( 1416) SS BOND : bond 0.00211 ( 6) SS BOND : angle 1.96211 ( 12) covalent geometry : bond 0.00325 ( 8626) covalent geometry : angle 0.59837 (11794) Misc. bond : bond 0.00012 ( 4) *********************** 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 204 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 156 time to evaluate : 0.884 Fit side-chains REVERT: A 274 ASN cc_start: 0.8399 (m-40) cc_final: 0.8123 (m110) REVERT: A 301 ASP cc_start: 0.7851 (t0) cc_final: 0.7503 (t0) REVERT: A 349 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8112 (p) REVERT: A 440 ARG cc_start: 0.7570 (mtt-85) cc_final: 0.7209 (mtp85) REVERT: A 484 ASP cc_start: 0.8000 (OUTLIER) cc_final: 0.7654 (t0) REVERT: A 496 VAL cc_start: 0.8587 (t) cc_final: 0.8380 (p) REVERT: A 528 ARG cc_start: 0.8175 (mmt-90) cc_final: 0.7810 (mtt180) REVERT: B 274 ASN cc_start: 0.8366 (m-40) cc_final: 0.8082 (m110) REVERT: B 301 ASP cc_start: 0.7817 (t0) cc_final: 0.7492 (t0) REVERT: B 349 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8080 (p) REVERT: B 440 ARG cc_start: 0.7560 (mtt-85) cc_final: 0.7247 (mtp85) REVERT: B 445 ARG cc_start: 0.8021 (mtm110) cc_final: 0.7642 (mtm110) REVERT: B 484 ASP cc_start: 0.7969 (OUTLIER) cc_final: 0.7593 (t0) REVERT: B 521 GLN cc_start: 0.8382 (OUTLIER) cc_final: 0.8153 (mp10) REVERT: B 528 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7803 (mtt180) outliers start: 48 outliers final: 25 residues processed: 182 average time/residue: 1.1956 time to fit residues: 232.0744 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 : 0.914 ------------------------------------------------------------------------------- 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 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 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 185 SER 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 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 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 102 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 97 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 77 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3363 r_free = 0.3363 target = 0.123445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.095656 restraints weight = 9926.262| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 2.06 r_work: 0.2936 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2799 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2799 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.3261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8648 Z= 0.135 Angle : 0.648 10.124 11842 Z= 0.297 Chirality : 0.042 0.168 1466 Planarity : 0.004 0.042 1404 Dihedral : 8.247 142.795 1648 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 4.20 % Allowed : 15.65 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.26), residues: 1070 helix: 1.99 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS A 547 PHE 0.010 0.001 PHE A 428 TYR 0.013 0.001 TYR B 216 ARG 0.004 0.000 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00223 ( 4) link_NAG-ASN : angle 4.14889 ( 12) link_ALPHA1-4 : bond 0.01661 ( 4) link_ALPHA1-4 : angle 2.05548 ( 12) link_BETA1-4 : bond 0.01440 ( 4) link_BETA1-4 : angle 6.09523 ( 12) hydrogen bonds : bond 0.03841 ( 496) hydrogen bonds : angle 3.78902 ( 1416) SS BOND : bond 0.00131 ( 6) SS BOND : angle 2.22588 ( 12) covalent geometry : bond 0.00314 ( 8626) covalent geometry : angle 0.59709 (11794) Misc. bond : bond 0.00005 ( 4) *********************** 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 187 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8420 (m-40) cc_final: 0.8112 (m110) REVERT: A 301 ASP cc_start: 0.7820 (t0) cc_final: 0.7469 (t0) REVERT: A 349 THR cc_start: 0.8426 (OUTLIER) cc_final: 0.8090 (p) REVERT: A 440 ARG cc_start: 0.7418 (mtt-85) cc_final: 0.7034 (mtp85) REVERT: A 484 ASP cc_start: 0.7998 (OUTLIER) cc_final: 0.7611 (t0) REVERT: A 528 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7797 (mtt180) REVERT: B 274 ASN cc_start: 0.8342 (m-40) cc_final: 0.8033 (m110) REVERT: B 301 ASP cc_start: 0.7828 (t0) cc_final: 0.7481 (t0) REVERT: B 349 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8053 (p) REVERT: B 440 ARG cc_start: 0.7404 (mtt-85) cc_final: 0.7033 (mtp85) REVERT: B 445 ARG cc_start: 0.8068 (mtm110) cc_final: 0.7739 (mtm110) REVERT: B 484 ASP cc_start: 0.7937 (OUTLIER) cc_final: 0.7563 (t0) REVERT: B 521 GLN cc_start: 0.8448 (OUTLIER) cc_final: 0.8046 (mp10) REVERT: B 528 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7777 (mtt180) outliers start: 37 outliers final: 21 residues processed: 170 average time/residue: 1.2480 time to fit residues: 226.0155 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 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 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 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 521 GLN 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 93 optimal weight: 1.9990 chunk 89 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 88 optimal weight: 4.9990 chunk 27 optimal weight: 0.8980 chunk 73 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3358 r_free = 0.3358 target = 0.123061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.095060 restraints weight = 9930.598| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.09 r_work: 0.2925 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3343 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= 0.143 Angle : 0.648 9.936 11842 Z= 0.302 Chirality : 0.042 0.168 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.452 141.988 1648 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 3.85 % Allowed : 16.21 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.26), residues: 1070 helix: 2.03 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 556 HIS 0.001 0.000 HIS B 547 PHE 0.010 0.001 PHE B 428 TYR 0.013 0.001 TYR B 216 ARG 0.006 0.000 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00195 ( 4) link_NAG-ASN : angle 4.16472 ( 12) link_ALPHA1-4 : bond 0.01632 ( 4) link_ALPHA1-4 : angle 2.37756 ( 12) link_BETA1-4 : bond 0.01466 ( 4) link_BETA1-4 : angle 5.92970 ( 12) hydrogen bonds : bond 0.03947 ( 496) hydrogen bonds : angle 3.80509 ( 1416) SS BOND : bond 0.00273 ( 6) SS BOND : angle 2.74411 ( 12) covalent geometry : bond 0.00341 ( 8626) covalent geometry : angle 0.59597 (11794) Misc. bond : bond 0.00008 ( 4) *********************** 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 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 147 time to evaluate : 0.835 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8419 (m-40) cc_final: 0.8134 (m110) REVERT: A 301 ASP cc_start: 0.7819 (t0) cc_final: 0.7465 (t0) REVERT: A 349 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8143 (p) REVERT: A 484 ASP cc_start: 0.8010 (OUTLIER) cc_final: 0.7667 (t0) REVERT: A 528 ARG cc_start: 0.8152 (mmt-90) cc_final: 0.7788 (mtt180) REVERT: B 274 ASN cc_start: 0.8379 (m-40) cc_final: 0.8097 (m110) REVERT: B 301 ASP cc_start: 0.7819 (t0) cc_final: 0.7472 (t0) REVERT: B 349 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8057 (p) REVERT: B 445 ARG cc_start: 0.8035 (mtm110) cc_final: 0.7663 (mtm110) REVERT: B 484 ASP cc_start: 0.7950 (OUTLIER) cc_final: 0.7566 (t0) REVERT: B 521 GLN cc_start: 0.8486 (OUTLIER) cc_final: 0.8059 (mp10) REVERT: B 528 ARG cc_start: 0.8155 (mmt-90) cc_final: 0.7783 (mtt180) outliers start: 34 outliers final: 24 residues processed: 166 average time/residue: 1.2354 time to fit residues: 217.4213 Evaluate side-chains 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 147 time to evaluate : 0.953 ------------------------------------------------------------------------------- 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 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 514 SER Chi-restraints excluded: chain A residue 587 MET 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 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 Chi-restraints excluded: chain B residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 5.9990 chunk 11 optimal weight: 0.7980 chunk 56 optimal weight: 4.9990 chunk 95 optimal weight: 0.7980 chunk 27 optimal weight: 0.0870 chunk 22 optimal weight: 0.0980 chunk 102 optimal weight: 5.9990 chunk 34 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3382 r_free = 0.3382 target = 0.124877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.096839 restraints weight = 9966.823| |-----------------------------------------------------------------------------| r_work (start): 0.3019 rms_B_bonded: 2.08 r_work: 0.2884 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2745 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2745 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8124 moved from start: 0.3417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8648 Z= 0.119 Angle : 0.612 9.677 11842 Z= 0.287 Chirality : 0.041 0.160 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.236 139.234 1648 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 2.83 % Allowed : 17.23 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.26), residues: 1070 helix: 2.28 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.09 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS A 547 PHE 0.008 0.001 PHE A 428 TYR 0.014 0.001 TYR B 216 ARG 0.005 0.001 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00284 ( 4) link_NAG-ASN : angle 3.88917 ( 12) link_ALPHA1-4 : bond 0.01460 ( 4) link_ALPHA1-4 : angle 1.99354 ( 12) link_BETA1-4 : bond 0.01479 ( 4) link_BETA1-4 : angle 5.77803 ( 12) hydrogen bonds : bond 0.03583 ( 496) hydrogen bonds : angle 3.72318 ( 1416) SS BOND : bond 0.00151 ( 6) SS BOND : angle 2.30767 ( 12) covalent geometry : bond 0.00263 ( 8626) covalent geometry : angle 0.56368 (11794) Misc. bond : bond 0.00015 ( 4) *********************** 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 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 145 time to evaluate : 0.978 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8281 (m-40) cc_final: 0.7983 (m110) REVERT: A 301 ASP cc_start: 0.7747 (t0) cc_final: 0.7325 (t0) REVERT: A 349 THR cc_start: 0.8388 (OUTLIER) cc_final: 0.8099 (p) REVERT: A 400 ASP cc_start: 0.8511 (t0) cc_final: 0.8233 (t0) REVERT: A 440 ARG cc_start: 0.7915 (mtp85) cc_final: 0.7378 (mtp85) REVERT: A 484 ASP cc_start: 0.7931 (OUTLIER) cc_final: 0.7533 (t0) REVERT: A 528 ARG cc_start: 0.8103 (mmt-90) cc_final: 0.7720 (mtt180) REVERT: B 274 ASN cc_start: 0.8245 (m-40) cc_final: 0.7952 (m110) REVERT: B 301 ASP cc_start: 0.7765 (t0) cc_final: 0.7417 (t0) REVERT: B 349 THR cc_start: 0.8386 (OUTLIER) cc_final: 0.8035 (p) REVERT: B 440 ARG cc_start: 0.7896 (mtp85) cc_final: 0.7340 (mmm-85) REVERT: B 445 ARG cc_start: 0.8010 (mtm110) cc_final: 0.7664 (mtm110) REVERT: B 484 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7499 (t0) REVERT: B 521 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7974 (mp10) REVERT: B 528 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7715 (mtt180) outliers start: 25 outliers final: 17 residues processed: 159 average time/residue: 1.3959 time to fit residues: 235.5998 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 142 time to evaluate : 1.322 ------------------------------------------------------------------------------- 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 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 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 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 98 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 41 optimal weight: 0.8980 chunk 11 optimal weight: 0.0570 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 18 optimal weight: 0.0570 chunk 100 optimal weight: 0.6980 overall best weight: 0.5216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3400 r_free = 0.3400 target = 0.126480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098613 restraints weight = 9901.154| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.06 r_work: 0.2975 rms_B_bonded: 2.53 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: 0.8156 moved from start: 0.3507 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= 0.114 Angle : 0.599 9.342 11842 Z= 0.282 Chirality : 0.040 0.154 1466 Planarity : 0.004 0.041 1404 Dihedral : 6.936 135.544 1648 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.61 % Allowed : 17.69 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.26), residues: 1070 helix: 2.38 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.10 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 547 PHE 0.009 0.001 PHE A 428 TYR 0.014 0.001 TYR B 613 ARG 0.007 0.001 ARG A 445 Details of bonding type rmsd link_NAG-ASN : bond 0.00275 ( 4) link_NAG-ASN : angle 3.82938 ( 12) link_ALPHA1-4 : bond 0.01275 ( 4) link_ALPHA1-4 : angle 1.99817 ( 12) link_BETA1-4 : bond 0.01452 ( 4) link_BETA1-4 : angle 5.59269 ( 12) hydrogen bonds : bond 0.03404 ( 496) hydrogen bonds : angle 3.65602 ( 1416) SS BOND : bond 0.00167 ( 6) SS BOND : angle 2.11084 ( 12) covalent geometry : bond 0.00256 ( 8626) covalent geometry : angle 0.55187 (11794) Misc. bond : bond 0.00016 ( 4) ********************** 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 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 147 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8337 (m-40) cc_final: 0.8034 (m110) REVERT: A 301 ASP cc_start: 0.7800 (t0) cc_final: 0.7375 (t0) REVERT: A 349 THR cc_start: 0.8318 (OUTLIER) cc_final: 0.8001 (p) REVERT: A 400 ASP cc_start: 0.8455 (t0) cc_final: 0.8188 (t0) REVERT: A 484 ASP cc_start: 0.7895 (OUTLIER) cc_final: 0.7521 (t0) REVERT: A 528 ARG cc_start: 0.8173 (mmt-90) cc_final: 0.7769 (mtt180) REVERT: B 274 ASN cc_start: 0.8295 (m-40) cc_final: 0.7996 (m110) REVERT: B 301 ASP cc_start: 0.7809 (t0) cc_final: 0.7457 (t0) REVERT: B 349 THR cc_start: 0.8370 (OUTLIER) cc_final: 0.8073 (p) REVERT: B 445 ARG cc_start: 0.8013 (mtm110) cc_final: 0.7660 (mtm110) REVERT: B 484 ASP cc_start: 0.7798 (OUTLIER) cc_final: 0.7413 (t0) REVERT: B 521 GLN cc_start: 0.8394 (OUTLIER) cc_final: 0.7891 (mp10) REVERT: B 528 ARG cc_start: 0.8179 (mmt-90) cc_final: 0.7790 (mtt180) outliers start: 23 outliers final: 16 residues processed: 161 average time/residue: 1.6479 time to fit residues: 281.5862 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 143 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 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 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 31 optimal weight: 0.0270 chunk 47 optimal weight: 3.9990 chunk 11 optimal weight: 0.0670 chunk 32 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3396 r_free = 0.3396 target = 0.126146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098049 restraints weight = 10074.835| |-----------------------------------------------------------------------------| r_work (start): 0.3097 rms_B_bonded: 2.08 r_work: 0.2971 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.3586 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= 0.113 Angle : 0.591 9.052 11842 Z= 0.279 Chirality : 0.040 0.153 1466 Planarity : 0.004 0.041 1404 Dihedral : 6.756 133.825 1648 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.83 % Allowed : 17.35 % Favored : 79.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1070 helix: 2.43 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -0.99 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 PHE 0.009 0.001 PHE B 428 TYR 0.013 0.001 TYR A 613 ARG 0.006 0.001 ARG B 191 Details of bonding type rmsd link_NAG-ASN : bond 0.00266 ( 4) link_NAG-ASN : angle 3.81374 ( 12) link_ALPHA1-4 : bond 0.01182 ( 4) link_ALPHA1-4 : angle 2.03770 ( 12) link_BETA1-4 : bond 0.01418 ( 4) link_BETA1-4 : angle 5.40632 ( 12) hydrogen bonds : bond 0.03355 ( 496) hydrogen bonds : angle 3.61614 ( 1416) SS BOND : bond 0.00170 ( 6) SS BOND : angle 2.05598 ( 12) covalent geometry : bond 0.00255 ( 8626) covalent geometry : angle 0.54593 (11794) Misc. bond : bond 0.00015 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6466.45 seconds wall clock time: 114 minutes 48.69 seconds (6888.69 seconds total)