Starting phenix.real_space_refine on Sat Aug 23 00:25:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kkr_0701/08_2025/6kkr_0701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkr_0701/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/6kkr_0701/08_2025/6kkr_0701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkr_0701/08_2025/6kkr_0701.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6kkr_0701/08_2025/6kkr_0701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkr_0701/08_2025/6kkr_0701.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen 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: 1.86, per 1000 atoms: 0.22 Number of scatterers: 8416 At special positions: 0 Unit cell: (75.97, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.89 Conformation dependent library (CDL) restraints added in 289.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.29 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.753A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 176 removed outlier: 7.052A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.661A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.679A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.623A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.593A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.405A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 536 removed outlier: 3.545A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix removed outlier: 3.893A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.753A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 176 removed outlier: 7.052A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.661A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.679A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.623A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.593A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.405A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 536 removed outlier: 3.545A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix removed outlier: 3.893A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329 496 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.45 Time building geometry restraints manager: 1.15 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.670 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.430 ------------------------------------------------------------------------------- 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 : 3.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.23 % Allowed : 2.38 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.53 (0.20), residues: 1070 helix: -2.09 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 528 TYR 0.027 0.003 TYR B 466 PHE 0.036 0.004 PHE A 473 TRP 0.029 0.003 TRP A 339 HIS 0.003 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00851 ( 8626) covalent geometry : angle 1.12315 (11794) SS BOND : bond 0.00615 ( 6) SS BOND : angle 2.32835 ( 12) hydrogen bonds : bond 0.20760 ( 496) hydrogen bonds : angle 7.18464 ( 1416) Misc. bond : bond 0.00749 ( 4) 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) link_NAG-ASN : bond 0.00482 ( 4) link_NAG-ASN : angle 9.10026 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 242 time to evaluate : 0.205 Fit side-chains REVERT: A 400 ASP cc_start: 0.8009 (t0) cc_final: 0.7794 (t0) REVERT: A 405 LYS cc_start: 0.8314 (tttp) cc_final: 0.8077 (tttp) REVERT: A 449 LYS cc_start: 0.8156 (tttp) cc_final: 0.7753 (ttmt) REVERT: A 488 ASP cc_start: 0.8046 (m-30) cc_final: 0.7657 (m-30) REVERT: A 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7093 (mtp85) REVERT: B 400 ASP cc_start: 0.7975 (t0) cc_final: 0.7766 (t0) REVERT: B 405 LYS cc_start: 0.8302 (tttp) cc_final: 0.8064 (tttp) REVERT: B 449 LYS cc_start: 0.8152 (tttp) cc_final: 0.7744 (ttmt) REVERT: B 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7098 (mtp85) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 0.4636 time to fit residues: 120.7506 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 : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 65 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 61 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.126907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.099063 restraints weight = 9803.707| |-----------------------------------------------------------------------------| r_work (start): 0.3068 rms_B_bonded: 2.06 r_work: 0.2939 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2800 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8648 Z= 0.140 Angle : 0.850 21.364 11842 Z= 0.365 Chirality : 0.058 1.023 1466 Planarity : 0.005 0.058 1404 Dihedral : 15.497 144.305 1650 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 3.63 % Allowed : 11.00 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.18 (0.24), residues: 1070 helix: 0.08 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.11 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 191 TYR 0.015 0.002 TYR B 292 PHE 0.012 0.001 PHE B 428 TRP 0.005 0.001 TRP B 381 HIS 0.001 0.000 HIS A 394 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 8626) covalent geometry : angle 0.72406 (11794) SS BOND : bond 0.00634 ( 6) SS BOND : angle 1.78654 ( 12) hydrogen bonds : bond 0.04574 ( 496) hydrogen bonds : angle 4.40506 ( 1416) Misc. bond : bond 0.00045 ( 4) link_ALPHA1-4 : bond 0.00726 ( 4) link_ALPHA1-4 : angle 2.12010 ( 12) link_BETA1-4 : bond 0.00978 ( 4) link_BETA1-4 : angle 7.76012 ( 12) link_NAG-ASN : bond 0.01363 ( 4) link_NAG-ASN : angle 11.36969 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 161 time to evaluate : 0.344 Fit side-chains REVERT: A 274 ASN cc_start: 0.8453 (m-40) cc_final: 0.8138 (m110) REVERT: A 276 PHE cc_start: 0.7666 (m-10) cc_final: 0.7450 (m-10) REVERT: A 400 ASP cc_start: 0.8708 (t0) cc_final: 0.8407 (t0) REVERT: A 445 ARG cc_start: 0.7845 (mtm110) cc_final: 0.7617 (mtm110) REVERT: A 528 ARG cc_start: 0.8115 (mmt-90) cc_final: 0.7648 (mtp85) REVERT: A 612 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8179 (ttmp) REVERT: B 274 ASN cc_start: 0.8421 (m-40) cc_final: 0.8093 (m110) REVERT: B 276 PHE cc_start: 0.7604 (m-10) cc_final: 0.7397 (m-10) REVERT: B 400 ASP cc_start: 0.8696 (t0) cc_final: 0.8394 (t0) REVERT: B 445 ARG cc_start: 0.8015 (mtm110) cc_final: 0.7665 (mtm110) REVERT: B 528 ARG cc_start: 0.8068 (mmt-90) cc_final: 0.7596 (mtp85) REVERT: B 612 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.8165 (ttmp) outliers start: 32 outliers final: 15 residues processed: 173 average time/residue: 0.5825 time to fit residues: 106.9519 Evaluate side-chains 151 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 134 time to evaluate : 0.329 ------------------------------------------------------------------------------- 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 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 39 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 61 optimal weight: 6.9990 chunk 7 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 337 GLN A 377 GLN A 606 ASN B 131 ASN B 337 GLN B 606 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.126465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098395 restraints weight = 9636.945| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.06 r_work: 0.2944 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.2582 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= 0.131 Angle : 0.723 11.398 11842 Z= 0.324 Chirality : 0.043 0.244 1466 Planarity : 0.005 0.049 1404 Dihedral : 12.996 145.056 1648 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.99 % Allowed : 10.54 % Favored : 84.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.25), residues: 1070 helix: 1.00 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.75 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.012 0.001 TYR A 292 PHE 0.012 0.001 PHE B 428 TRP 0.007 0.001 TRP B 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00285 ( 8626) covalent geometry : angle 0.65304 (11794) SS BOND : bond 0.00342 ( 6) SS BOND : angle 1.83234 ( 12) hydrogen bonds : bond 0.04202 ( 496) hydrogen bonds : angle 4.04969 ( 1416) Misc. bond : bond 0.00016 ( 4) link_ALPHA1-4 : bond 0.01158 ( 4) link_ALPHA1-4 : angle 1.80801 ( 12) link_BETA1-4 : bond 0.02047 ( 4) link_BETA1-4 : angle 7.71228 ( 12) link_NAG-ASN : bond 0.01132 ( 4) link_NAG-ASN : angle 5.55988 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 150 time to evaluate : 0.258 Fit side-chains REVERT: A 274 ASN cc_start: 0.8421 (m-40) cc_final: 0.8103 (m110) REVERT: A 276 PHE cc_start: 0.7670 (m-10) cc_final: 0.7466 (m-10) REVERT: A 400 ASP cc_start: 0.8582 (t0) cc_final: 0.8327 (t0) REVERT: A 443 ASP cc_start: 0.7995 (m-30) cc_final: 0.7067 (t0) REVERT: A 445 ARG cc_start: 0.7865 (mtm110) cc_final: 0.7638 (mtm110) REVERT: A 496 VAL cc_start: 0.8469 (OUTLIER) cc_final: 0.8195 (p) REVERT: A 528 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7662 (mtp85) REVERT: B 274 ASN cc_start: 0.8444 (m-40) cc_final: 0.8114 (m110) REVERT: B 400 ASP cc_start: 0.8580 (t0) cc_final: 0.8330 (t0) REVERT: B 435 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8568 (mmt) REVERT: B 443 ASP cc_start: 0.7998 (m-30) cc_final: 0.7095 (t0) REVERT: B 445 ARG cc_start: 0.8048 (mtm110) cc_final: 0.7687 (mtm110) REVERT: B 496 VAL cc_start: 0.8532 (t) cc_final: 0.8270 (p) REVERT: B 528 ARG cc_start: 0.8127 (mmt-90) cc_final: 0.7659 (mtp85) outliers start: 44 outliers final: 21 residues processed: 172 average time/residue: 0.5504 time to fit residues: 100.6221 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 : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU 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 A residue 496 VAL Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 281 LEU 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 435 MET Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 69 optimal weight: 0.0870 chunk 75 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 20 optimal weight: 8.9990 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 74 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 89 optimal weight: 1.9990 overall best weight: 0.8960 ------------------------------------------------------------------------------- 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 B 606 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.125967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.097283 restraints weight = 9886.428| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 2.15 r_work: 0.2961 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8648 Z= 0.127 Angle : 0.649 9.169 11842 Z= 0.295 Chirality : 0.042 0.174 1466 Planarity : 0.004 0.045 1404 Dihedral : 11.703 144.225 1648 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.44 % Allowed : 10.20 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.26), residues: 1070 helix: 1.44 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.56 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 317 TYR 0.012 0.001 TYR A 292 PHE 0.011 0.001 PHE A 428 TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 8626) covalent geometry : angle 0.59737 (11794) SS BOND : bond 0.00181 ( 6) SS BOND : angle 2.02571 ( 12) hydrogen bonds : bond 0.03937 ( 496) hydrogen bonds : angle 3.94093 ( 1416) Misc. bond : bond 0.00014 ( 4) link_ALPHA1-4 : bond 0.01197 ( 4) link_ALPHA1-4 : angle 2.01668 ( 12) link_BETA1-4 : bond 0.00404 ( 4) link_BETA1-4 : angle 6.14910 ( 12) link_NAG-ASN : bond 0.00384 ( 4) link_NAG-ASN : angle 4.36829 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 161 time to evaluate : 0.308 Fit side-chains REVERT: A 274 ASN cc_start: 0.8407 (m-40) cc_final: 0.8116 (m110) REVERT: A 276 PHE cc_start: 0.7642 (m-10) cc_final: 0.7422 (m-10) REVERT: A 349 THR cc_start: 0.8518 (OUTLIER) cc_final: 0.8216 (p) REVERT: A 400 ASP cc_start: 0.8612 (t0) cc_final: 0.8392 (t0) REVERT: A 443 ASP cc_start: 0.7999 (m-30) cc_final: 0.7137 (t0) REVERT: A 445 ARG cc_start: 0.7863 (mtm110) cc_final: 0.7609 (mtm110) REVERT: A 488 ASP cc_start: 0.8149 (m-30) cc_final: 0.7496 (m-30) REVERT: A 496 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8259 (p) REVERT: A 528 ARG cc_start: 0.8203 (mmt-90) cc_final: 0.7779 (mtt90) REVERT: B 274 ASN cc_start: 0.8365 (m-40) cc_final: 0.8066 (m110) REVERT: B 349 THR cc_start: 0.8510 (OUTLIER) cc_final: 0.8191 (p) REVERT: B 443 ASP cc_start: 0.7994 (m-30) cc_final: 0.7113 (t0) REVERT: B 445 ARG cc_start: 0.8047 (mtm110) cc_final: 0.7667 (mtm110) REVERT: B 496 VAL cc_start: 0.8563 (t) cc_final: 0.8323 (p) REVERT: B 528 ARG cc_start: 0.8212 (mmt-90) cc_final: 0.7763 (mtp85) outliers start: 48 outliers final: 28 residues processed: 184 average time/residue: 0.5675 time to fit residues: 111.2478 Evaluate side-chains 188 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 157 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 281 LEU 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 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 496 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 281 LEU 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 418 THR Chi-restraints excluded: chain B residue 434 ILE 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 538 ILE 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 45 optimal weight: 1.9990 chunk 46 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 chunk 32 optimal weight: 0.0770 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 89 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 98 optimal weight: 4.9990 overall best weight: 1.0342 ------------------------------------------------------------------------------- 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 B 606 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.124545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096336 restraints weight = 9885.153| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.07 r_work: 0.2970 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2832 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8648 Z= 0.133 Angle : 0.646 8.896 11842 Z= 0.295 Chirality : 0.042 0.177 1466 Planarity : 0.004 0.043 1404 Dihedral : 10.191 144.234 1648 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 5.78 % Allowed : 11.00 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.78 (0.26), residues: 1070 helix: 1.72 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.41 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 440 TYR 0.013 0.001 TYR A 216 PHE 0.011 0.001 PHE B 428 TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00312 ( 8626) covalent geometry : angle 0.59437 (11794) SS BOND : bond 0.00262 ( 6) SS BOND : angle 2.31167 ( 12) hydrogen bonds : bond 0.03934 ( 496) hydrogen bonds : angle 3.82217 ( 1416) Misc. bond : bond 0.00009 ( 4) link_ALPHA1-4 : bond 0.01469 ( 4) link_ALPHA1-4 : angle 1.90243 ( 12) link_BETA1-4 : bond 0.00832 ( 4) link_BETA1-4 : angle 5.96685 ( 12) link_NAG-ASN : bond 0.00168 ( 4) link_NAG-ASN : angle 4.46319 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 165 time to evaluate : 0.309 Fit side-chains REVERT: A 274 ASN cc_start: 0.8398 (m-40) cc_final: 0.8119 (m110) REVERT: A 301 ASP cc_start: 0.7833 (t0) cc_final: 0.7405 (t0) REVERT: A 349 THR cc_start: 0.8508 (OUTLIER) cc_final: 0.8201 (p) REVERT: A 443 ASP cc_start: 0.8018 (m-30) cc_final: 0.7179 (t0) REVERT: A 488 ASP cc_start: 0.8147 (m-30) cc_final: 0.7513 (m-30) REVERT: A 496 VAL cc_start: 0.8585 (OUTLIER) cc_final: 0.8362 (p) REVERT: A 528 ARG cc_start: 0.8185 (mmt-90) cc_final: 0.7791 (mtt180) REVERT: B 274 ASN cc_start: 0.8380 (m-40) cc_final: 0.8098 (m110) REVERT: B 301 ASP cc_start: 0.7814 (t0) cc_final: 0.7488 (t0) REVERT: B 349 THR cc_start: 0.8473 (OUTLIER) cc_final: 0.8130 (p) REVERT: B 443 ASP cc_start: 0.7882 (m-30) cc_final: 0.7129 (t0) REVERT: B 445 ARG cc_start: 0.7953 (mtm110) cc_final: 0.7677 (mtm110) REVERT: B 496 VAL cc_start: 0.8587 (t) cc_final: 0.8385 (p) REVERT: B 528 ARG cc_start: 0.8196 (mmt-90) cc_final: 0.7796 (mtt90) outliers start: 51 outliers final: 25 residues processed: 190 average time/residue: 0.6308 time to fit residues: 127.0920 Evaluate side-chains 182 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 154 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 158 LEU Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 496 VAL 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 158 LEU Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 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 492 ARG Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 38 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 76 optimal weight: 7.9990 chunk 5 optimal weight: 5.9990 chunk 1 optimal weight: 0.9980 chunk 87 optimal weight: 0.6980 chunk 69 optimal weight: 0.9980 chunk 31 optimal weight: 0.7980 chunk 99 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 B 606 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3393 r_free = 0.3393 target = 0.125281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.097367 restraints weight = 9809.137| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.04 r_work: 0.2983 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.3130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8648 Z= 0.123 Angle : 0.635 9.019 11842 Z= 0.290 Chirality : 0.041 0.169 1466 Planarity : 0.004 0.042 1404 Dihedral : 9.413 142.060 1648 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.88 % Allowed : 13.61 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.26), residues: 1070 helix: 1.88 (0.20), residues: 652 sheet: None (None), residues: 0 loop : -1.31 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 191 TYR 0.013 0.001 TYR A 216 PHE 0.010 0.001 PHE A 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 394 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8626) covalent geometry : angle 0.58622 (11794) SS BOND : bond 0.00126 ( 6) SS BOND : angle 1.80495 ( 12) hydrogen bonds : bond 0.03699 ( 496) hydrogen bonds : angle 3.74022 ( 1416) Misc. bond : bond 0.00005 ( 4) link_ALPHA1-4 : bond 0.01462 ( 4) link_ALPHA1-4 : angle 2.05108 ( 12) link_BETA1-4 : bond 0.00882 ( 4) link_BETA1-4 : angle 5.95684 ( 12) link_NAG-ASN : bond 0.00176 ( 4) link_NAG-ASN : angle 4.16073 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 156 time to evaluate : 0.317 Fit side-chains REVERT: A 274 ASN cc_start: 0.8397 (m-40) cc_final: 0.8113 (m110) REVERT: A 301 ASP cc_start: 0.7801 (t0) cc_final: 0.7449 (t0) REVERT: A 349 THR cc_start: 0.8460 (OUTLIER) cc_final: 0.8141 (p) REVERT: A 443 ASP cc_start: 0.8010 (m-30) cc_final: 0.7142 (t0) REVERT: A 484 ASP cc_start: 0.7947 (OUTLIER) cc_final: 0.7603 (t0) REVERT: A 496 VAL cc_start: 0.8597 (OUTLIER) cc_final: 0.8377 (p) REVERT: A 528 ARG cc_start: 0.8170 (mmt-90) cc_final: 0.7781 (mtt180) REVERT: B 274 ASN cc_start: 0.8345 (m-40) cc_final: 0.8058 (m110) REVERT: B 301 ASP cc_start: 0.7825 (t0) cc_final: 0.7486 (t0) REVERT: B 349 THR cc_start: 0.8374 (OUTLIER) cc_final: 0.8037 (p) REVERT: B 443 ASP cc_start: 0.8086 (m-30) cc_final: 0.7299 (t0) REVERT: B 445 ARG cc_start: 0.7923 (mtm110) cc_final: 0.7660 (mtm110) REVERT: B 484 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7612 (t0) REVERT: B 496 VAL cc_start: 0.8593 (OUTLIER) cc_final: 0.8391 (p) REVERT: B 528 ARG cc_start: 0.8182 (mmt-90) cc_final: 0.7802 (mtt180) outliers start: 43 outliers final: 18 residues processed: 180 average time/residue: 0.6107 time to fit residues: 116.7667 Evaluate side-chains 178 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 154 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 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 496 VAL Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 62 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 84 optimal weight: 0.3980 chunk 78 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 27 optimal weight: 0.4980 chunk 56 optimal weight: 0.0670 chunk 42 optimal weight: 0.8980 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 606 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.126607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098414 restraints weight = 9938.024| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.08 r_work: 0.2937 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.3276 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= 0.117 Angle : 0.621 8.801 11842 Z= 0.283 Chirality : 0.040 0.159 1466 Planarity : 0.004 0.041 1404 Dihedral : 8.188 138.948 1648 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.20 % Allowed : 15.42 % Favored : 80.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1070 helix: 2.15 (0.20), residues: 656 sheet: None (None), residues: 0 loop : -1.16 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.013 0.001 TYR A 216 PHE 0.010 0.001 PHE A 428 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 615 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 8626) covalent geometry : angle 0.57224 (11794) SS BOND : bond 0.00350 ( 6) SS BOND : angle 1.94905 ( 12) hydrogen bonds : bond 0.03461 ( 496) hydrogen bonds : angle 3.67823 ( 1416) Misc. bond : bond 0.00010 ( 4) link_ALPHA1-4 : bond 0.01684 ( 4) link_ALPHA1-4 : angle 2.01960 ( 12) link_BETA1-4 : bond 0.00903 ( 4) link_BETA1-4 : angle 5.90443 ( 12) link_NAG-ASN : bond 0.00269 ( 4) link_NAG-ASN : angle 4.01874 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 162 time to evaluate : 0.374 Fit side-chains REVERT: A 274 ASN cc_start: 0.8311 (m-40) cc_final: 0.8034 (m110) REVERT: A 301 ASP cc_start: 0.7739 (t0) cc_final: 0.7319 (t0) REVERT: A 349 THR cc_start: 0.8420 (OUTLIER) cc_final: 0.8123 (p) REVERT: A 443 ASP cc_start: 0.7874 (m-30) cc_final: 0.6990 (t0) REVERT: A 484 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7463 (t0) REVERT: A 488 ASP cc_start: 0.8059 (m-30) cc_final: 0.7085 (m-30) REVERT: A 496 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8323 (p) REVERT: A 528 ARG cc_start: 0.8108 (mmt-90) cc_final: 0.7702 (mtt180) REVERT: B 274 ASN cc_start: 0.8267 (m-40) cc_final: 0.7976 (m110) REVERT: B 301 ASP cc_start: 0.7774 (t0) cc_final: 0.7421 (t0) REVERT: B 349 THR cc_start: 0.8463 (OUTLIER) cc_final: 0.8102 (p) REVERT: B 443 ASP cc_start: 0.8030 (m-30) cc_final: 0.7330 (t0) REVERT: B 445 ARG cc_start: 0.7889 (mtm110) cc_final: 0.7642 (mtm110) REVERT: B 484 ASP cc_start: 0.7873 (OUTLIER) cc_final: 0.7489 (t0) REVERT: B 496 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8322 (p) REVERT: B 528 ARG cc_start: 0.8114 (mmt-90) cc_final: 0.7691 (mtt180) outliers start: 37 outliers final: 19 residues processed: 181 average time/residue: 0.5665 time to fit residues: 109.3478 Evaluate side-chains 171 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 146 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 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 496 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 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 496 VAL Chi-restraints excluded: chain B residue 514 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 60 optimal weight: 0.9980 chunk 91 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 88 optimal weight: 3.9990 chunk 23 optimal weight: 7.9990 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 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 = 0.3343 r_free = 0.3343 target = 0.121629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.093766 restraints weight = 9884.349| |-----------------------------------------------------------------------------| r_work (start): 0.3048 rms_B_bonded: 2.06 r_work: 0.2917 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2777 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 8648 Z= 0.176 Angle : 0.691 9.000 11842 Z= 0.322 Chirality : 0.043 0.176 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.743 142.038 1648 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 4.54 % Allowed : 15.76 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.11 (0.26), residues: 1070 helix: 1.85 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.17 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 445 TYR 0.015 0.002 TYR B 411 PHE 0.015 0.002 PHE B 428 TRP 0.008 0.001 TRP A 556 HIS 0.002 0.001 HIS A 547 Details of bonding type rmsd covalent geometry : bond 0.00434 ( 8626) covalent geometry : angle 0.63854 (11794) SS BOND : bond 0.00397 ( 6) SS BOND : angle 3.17430 ( 12) hydrogen bonds : bond 0.04316 ( 496) hydrogen bonds : angle 3.84076 ( 1416) Misc. bond : bond 0.00027 ( 4) link_ALPHA1-4 : bond 0.01714 ( 4) link_ALPHA1-4 : angle 2.17712 ( 12) link_BETA1-4 : bond 0.00823 ( 4) link_BETA1-4 : angle 6.02100 ( 12) link_NAG-ASN : bond 0.00134 ( 4) link_NAG-ASN : angle 4.46438 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 155 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8390 (m-40) cc_final: 0.8119 (m110) REVERT: A 301 ASP cc_start: 0.7848 (t0) cc_final: 0.7488 (t0) REVERT: A 349 THR cc_start: 0.8454 (OUTLIER) cc_final: 0.8135 (p) REVERT: A 484 ASP cc_start: 0.8025 (OUTLIER) cc_final: 0.7671 (t0) REVERT: A 496 VAL cc_start: 0.8566 (OUTLIER) cc_final: 0.8361 (p) REVERT: A 528 ARG cc_start: 0.8180 (mmt-90) cc_final: 0.7803 (mtt180) REVERT: B 274 ASN cc_start: 0.8376 (m-40) cc_final: 0.8094 (m110) REVERT: B 301 ASP cc_start: 0.7889 (t0) cc_final: 0.7528 (t0) REVERT: B 349 THR cc_start: 0.8390 (OUTLIER) cc_final: 0.8032 (p) REVERT: B 445 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7706 (mtm110) REVERT: B 484 ASP cc_start: 0.8006 (OUTLIER) cc_final: 0.7654 (t0) REVERT: B 528 ARG cc_start: 0.8192 (mmt-90) cc_final: 0.7819 (mtt180) outliers start: 40 outliers final: 22 residues processed: 177 average time/residue: 0.6089 time to fit residues: 114.3693 Evaluate side-chains 179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 152 time to evaluate : 0.296 ------------------------------------------------------------------------------- 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 496 VAL Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 587 MET Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 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 587 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 94 optimal weight: 0.6980 chunk 101 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN B 131 ASN B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3375 r_free = 0.3375 target = 0.124115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.096291 restraints weight = 9871.746| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 2.06 r_work: 0.2875 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.3396 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8648 Z= 0.124 Angle : 0.631 8.911 11842 Z= 0.295 Chirality : 0.041 0.162 1466 Planarity : 0.004 0.040 1404 Dihedral : 7.438 140.003 1648 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 3.63 % Allowed : 17.46 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.39 (0.26), residues: 1070 helix: 2.16 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.20 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 191 TYR 0.013 0.001 TYR A 216 PHE 0.009 0.001 PHE B 211 TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 8626) covalent geometry : angle 0.58074 (11794) SS BOND : bond 0.00159 ( 6) SS BOND : angle 2.46063 ( 12) hydrogen bonds : bond 0.03745 ( 496) hydrogen bonds : angle 3.72119 ( 1416) Misc. bond : bond 0.00009 ( 4) link_ALPHA1-4 : bond 0.01540 ( 4) link_ALPHA1-4 : angle 2.04989 ( 12) link_BETA1-4 : bond 0.00939 ( 4) link_BETA1-4 : angle 5.92817 ( 12) link_NAG-ASN : bond 0.00212 ( 4) link_NAG-ASN : angle 4.06107 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 149 time to evaluate : 0.364 Fit side-chains REVERT: A 274 ASN cc_start: 0.8271 (m-40) cc_final: 0.7990 (m110) REVERT: A 301 ASP cc_start: 0.7759 (t0) cc_final: 0.7399 (t0) REVERT: A 349 THR cc_start: 0.8395 (OUTLIER) cc_final: 0.8091 (p) REVERT: A 443 ASP cc_start: 0.8132 (m-30) cc_final: 0.7327 (t0) REVERT: A 445 ARG cc_start: 0.7719 (mtm110) cc_final: 0.7460 (mtm110) REVERT: A 484 ASP cc_start: 0.7964 (OUTLIER) cc_final: 0.7571 (t0) REVERT: A 521 GLN cc_start: 0.8396 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: A 528 ARG cc_start: 0.8098 (mmt-90) cc_final: 0.7711 (mtt180) REVERT: A 647 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5670 (mtp) REVERT: B 274 ASN cc_start: 0.8313 (m-40) cc_final: 0.8031 (m110) REVERT: B 301 ASP cc_start: 0.7807 (t0) cc_final: 0.7444 (t0) REVERT: B 349 THR cc_start: 0.8346 (OUTLIER) cc_final: 0.7997 (p) REVERT: B 440 ARG cc_start: 0.7694 (mtp180) cc_final: 0.7414 (mtp85) REVERT: B 443 ASP cc_start: 0.8100 (m-30) cc_final: 0.7271 (t0) REVERT: B 445 ARG cc_start: 0.7916 (mtm110) cc_final: 0.7642 (mtm110) REVERT: B 484 ASP cc_start: 0.7933 (OUTLIER) cc_final: 0.7529 (t0) REVERT: B 521 GLN cc_start: 0.8392 (OUTLIER) cc_final: 0.8011 (mp10) REVERT: B 528 ARG cc_start: 0.8117 (mmt-90) cc_final: 0.7717 (mtt180) REVERT: B 647 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5696 (mtp) outliers start: 32 outliers final: 17 residues processed: 166 average time/residue: 0.6460 time to fit residues: 113.5513 Evaluate side-chains 173 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 148 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 647 MET 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 Chi-restraints excluded: chain B residue 647 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 51 optimal weight: 0.9980 chunk 49 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 25 optimal weight: 0.0980 chunk 102 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 0.0870 chunk 32 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3398 r_free = 0.3398 target = 0.125954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.097985 restraints weight = 9913.655| |-----------------------------------------------------------------------------| r_work (start): 0.3035 rms_B_bonded: 2.07 r_work: 0.2903 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.3517 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= 0.115 Angle : 0.603 8.710 11842 Z= 0.283 Chirality : 0.040 0.150 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.075 135.982 1648 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.29 % Allowed : 17.91 % Favored : 78.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.60 (0.26), residues: 1070 helix: 2.34 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.15 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 445 TYR 0.013 0.001 TYR A 216 PHE 0.009 0.001 PHE A 428 TRP 0.007 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 8626) covalent geometry : angle 0.55371 (11794) SS BOND : bond 0.00173 ( 6) SS BOND : angle 2.16528 ( 12) hydrogen bonds : bond 0.03430 ( 496) hydrogen bonds : angle 3.62892 ( 1416) Misc. bond : bond 0.00018 ( 4) link_ALPHA1-4 : bond 0.01293 ( 4) link_ALPHA1-4 : angle 1.97012 ( 12) link_BETA1-4 : bond 0.00953 ( 4) link_BETA1-4 : angle 5.85442 ( 12) link_NAG-ASN : bond 0.00219 ( 4) link_NAG-ASN : angle 3.88846 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8293 (m-40) cc_final: 0.8021 (m110) REVERT: A 301 ASP cc_start: 0.7775 (t0) cc_final: 0.7336 (t0) REVERT: A 349 THR cc_start: 0.8298 (OUTLIER) cc_final: 0.7997 (p) REVERT: A 443 ASP cc_start: 0.8023 (m-30) cc_final: 0.7056 (t0) REVERT: A 445 ARG cc_start: 0.7693 (mtm110) cc_final: 0.7455 (mtm110) REVERT: A 484 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7483 (t0) REVERT: A 521 GLN cc_start: 0.8428 (OUTLIER) cc_final: 0.8042 (mp10) REVERT: A 528 ARG cc_start: 0.8129 (mmt-90) cc_final: 0.7696 (mtt180) REVERT: A 647 MET cc_start: 0.6217 (OUTLIER) cc_final: 0.5614 (mtp) REVERT: B 274 ASN cc_start: 0.8258 (m-40) cc_final: 0.7957 (m110) REVERT: B 301 ASP cc_start: 0.7728 (t0) cc_final: 0.7372 (t0) REVERT: B 349 THR cc_start: 0.8289 (OUTLIER) cc_final: 0.7964 (p) REVERT: B 440 ARG cc_start: 0.7776 (mtp180) cc_final: 0.7249 (mtp85) REVERT: B 445 ARG cc_start: 0.7919 (mtm110) cc_final: 0.7637 (mtm110) REVERT: B 484 ASP cc_start: 0.7820 (OUTLIER) cc_final: 0.7423 (t0) REVERT: B 521 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.8020 (mp10) REVERT: B 528 ARG cc_start: 0.8118 (mmt-90) cc_final: 0.7714 (mtt180) outliers start: 29 outliers final: 19 residues processed: 168 average time/residue: 0.6214 time to fit residues: 110.5200 Evaluate side-chains 168 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 142 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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 321 ASP 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 514 SER Chi-restraints excluded: chain A residue 521 GLN Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 262 MET 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 15 optimal weight: 2.9990 chunk 76 optimal weight: 0.4980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 chunk 80 optimal weight: 0.0370 chunk 11 optimal weight: 0.0270 chunk 77 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.3214 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.126899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.098986 restraints weight = 9903.600| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.06 r_work: 0.2985 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 8648 Z= 0.111 Angle : 0.596 8.635 11842 Z= 0.280 Chirality : 0.040 0.153 1466 Planarity : 0.004 0.041 1404 Dihedral : 6.973 134.604 1648 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.95 % Allowed : 17.80 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.27), residues: 1070 helix: 2.43 (0.20), residues: 662 sheet: None (None), residues: 0 loop : -1.11 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 191 TYR 0.014 0.001 TYR A 613 PHE 0.011 0.001 PHE A 320 TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 Details of bonding type rmsd covalent geometry : bond 0.00240 ( 8626) covalent geometry : angle 0.54717 (11794) SS BOND : bond 0.00107 ( 6) SS BOND : angle 2.03331 ( 12) hydrogen bonds : bond 0.03288 ( 496) hydrogen bonds : angle 3.59458 ( 1416) Misc. bond : bond 0.00025 ( 4) link_ALPHA1-4 : bond 0.01246 ( 4) link_ALPHA1-4 : angle 2.05104 ( 12) link_BETA1-4 : bond 0.00969 ( 4) link_BETA1-4 : angle 5.80228 ( 12) link_NAG-ASN : bond 0.00264 ( 4) link_NAG-ASN : angle 3.81712 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3151.22 seconds wall clock time: 54 minutes 25.29 seconds (3265.29 seconds total)