Starting phenix.real_space_refine on Thu Feb 13 06:44:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.cif Found real_map, /net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.map" model { file = "/net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6kkr_0701/02_2025/6kkr_0701.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 Cl 4 4.86 5 C 5544 2.51 5 N 1284 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 8416 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "B" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 537, 4068 Classifications: {'peptide': 537} Link IDs: {'PTRANS': 26, 'TRANS': 510} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'BGC': 1, 'GLC': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 40 Unusual residues: {' K': 1, ' CL': 2, 'DU0': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 5.46, per 1000 atoms: 0.65 Number of scatterers: 8416 At special positions: 0 Unit cell: (75.97, 101.65, 102.72, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 Cl 4 17.00 S 68 16.00 O 1514 8.00 N 1284 7.00 C 5544 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 163 " - pdb=" SG CYS A 626 " distance=2.02 Simple disulfide: pdb=" SG CYS A 308 " - pdb=" SG CYS A 323 " distance=2.03 Simple disulfide: pdb=" SG CYS A 343 " - pdb=" SG CYS A 353 " distance=2.03 Simple disulfide: pdb=" SG CYS B 163 " - pdb=" SG CYS B 626 " distance=2.02 Simple disulfide: pdb=" SG CYS B 308 " - pdb=" SG CYS B 323 " distance=2.03 Simple disulfide: pdb=" SG CYS B 343 " - pdb=" SG CYS B 353 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Links applied ALPHA1-4 " BGC E 1 " - " GLC E 2 " " BGC F 1 " - " GLC F 2 " " BGC I 1 " - " GLC I 2 " " BGC J 1 " - " GLC J 2 " BETA1-4 " NAG C 1 " - " NAG C 2 " " NAG D 1 " - " NAG D 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " NAG-ASN " NAG C 1 " - " ASN A 312 " " NAG D 1 " - " ASN A 361 " " NAG G 1 " - " ASN B 312 " " NAG H 1 " - " ASN B 361 " Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.76 Conformation dependent library (CDL) restraints added in 1.2 seconds 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1968 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 4 sheets defined 71.3% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 124 through 133 removed outlier: 3.753A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 140 through 176 removed outlier: 7.052A pdb=" N VAL A 150 " --> pdb=" O GLY A 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU A 151 " --> pdb=" O THR A 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS A 163 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 164 " --> pdb=" O CYS A 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU A 165 " --> pdb=" O CYS A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE A 189 " --> pdb=" O SER A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA A 214 " --> pdb=" O THR A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL A 253 " --> pdb=" O ASN A 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU A 264 " --> pdb=" O THR A 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 276 Processing helix chain 'A' and resid 278 through 301 removed outlier: 3.661A pdb=" N VAL A 284 " --> pdb=" O PHE A 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE A 291 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE A 299 " --> pdb=" O GLY A 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE A 300 " --> pdb=" O ILE A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER A 340 " --> pdb=" O THR A 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE A 342 " --> pdb=" O LEU A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 360 Processing helix chain 'A' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU A 378 " --> pdb=" O GLY A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 408 Processing helix chain 'A' and resid 419 through 428 removed outlier: 3.679A pdb=" N GLY A 425 " --> pdb=" O THR A 421 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 431 No H-bonds generated for 'chain 'A' and resid 429 through 431' Processing helix chain 'A' and resid 434 through 438 removed outlier: 3.623A pdb=" N SER A 438 " --> pdb=" O MET A 435 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE A 451 " --> pdb=" O ALA A 447 " (cutoff:3.500A) Proline residue: A 452 - end of helix removed outlier: 3.593A pdb=" N ILE A 456 " --> pdb=" O PRO A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 483 Processing helix chain 'A' and resid 484 through 488 removed outlier: 4.405A pdb=" N ASP A 488 " --> pdb=" O LYS A 485 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 500 Processing helix chain 'A' and resid 504 through 536 removed outlier: 3.545A pdb=" N VAL A 508 " --> pdb=" O PRO A 504 " (cutoff:3.500A) Proline residue: A 527 - end of helix Processing helix chain 'A' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL A 544 " --> pdb=" O PHE A 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS A 547 " --> pdb=" O VAL A 544 " (cutoff:3.500A) Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU A 559 " --> pdb=" O THR A 555 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY A 568 " --> pdb=" O ILE A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 573 through 602 Proline residue: A 579 - end of helix removed outlier: 3.893A pdb=" N GLN A 599 " --> pdb=" O ALA A 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR A 600 " --> pdb=" O CYS A 596 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER A 619 " --> pdb=" O HIS A 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 630 " --> pdb=" O CYS A 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER A 634 " --> pdb=" O MET A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU A 643 " --> pdb=" O LEU A 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS A 650 " --> pdb=" O GLY A 646 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 124 Processing helix chain 'B' and resid 124 through 133 removed outlier: 3.753A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 140 Processing helix chain 'B' and resid 140 through 176 removed outlier: 7.052A pdb=" N VAL B 150 " --> pdb=" O GLY B 146 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N LEU B 151 " --> pdb=" O THR B 147 " (cutoff:3.500A) removed outlier: 4.094A pdb=" N GLN B 152 " --> pdb=" O ALA B 148 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N CYS B 163 " --> pdb=" O ILE B 159 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR B 164 " --> pdb=" O CYS B 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU B 165 " --> pdb=" O CYS B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 185 through 194 removed outlier: 3.504A pdb=" N ILE B 189 " --> pdb=" O SER B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 227 removed outlier: 3.694A pdb=" N ALA B 200 " --> pdb=" O GLU B 196 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA B 214 " --> pdb=" O THR B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 244 through 269 removed outlier: 3.713A pdb=" N VAL B 253 " --> pdb=" O ASN B 249 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU B 264 " --> pdb=" O THR B 260 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL B 266 " --> pdb=" O MET B 262 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 278 through 301 removed outlier: 3.661A pdb=" N VAL B 284 " --> pdb=" O PHE B 280 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE B 291 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE B 299 " --> pdb=" O GLY B 295 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N PHE B 300 " --> pdb=" O ILE B 296 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 344 removed outlier: 3.640A pdb=" N SER B 340 " --> pdb=" O THR B 336 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N PHE B 342 " --> pdb=" O LEU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 360 Processing helix chain 'B' and resid 372 through 379 removed outlier: 3.602A pdb=" N GLU B 378 " --> pdb=" O GLY B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 Processing helix chain 'B' and resid 419 through 428 removed outlier: 3.679A pdb=" N GLY B 425 " --> pdb=" O THR B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 429 through 431 No H-bonds generated for 'chain 'B' and resid 429 through 431' Processing helix chain 'B' and resid 434 through 438 removed outlier: 3.623A pdb=" N SER B 438 " --> pdb=" O MET B 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 477 removed outlier: 3.640A pdb=" N ILE B 451 " --> pdb=" O ALA B 447 " (cutoff:3.500A) Proline residue: B 452 - end of helix removed outlier: 3.593A pdb=" N ILE B 456 " --> pdb=" O PRO B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 483 Processing helix chain 'B' and resid 484 through 488 removed outlier: 4.405A pdb=" N ASP B 488 " --> pdb=" O LYS B 485 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 Processing helix chain 'B' and resid 504 through 536 removed outlier: 3.545A pdb=" N VAL B 508 " --> pdb=" O PRO B 504 " (cutoff:3.500A) Proline residue: B 527 - end of helix Processing helix chain 'B' and resid 539 through 547 removed outlier: 5.316A pdb=" N VAL B 544 " --> pdb=" O PHE B 541 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS B 547 " --> pdb=" O VAL B 544 " (cutoff:3.500A) Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.675A pdb=" N LEU B 559 " --> pdb=" O THR B 555 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLY B 568 " --> pdb=" O ILE B 564 " (cutoff:3.500A) Processing helix chain 'B' and resid 573 through 602 Proline residue: B 579 - end of helix removed outlier: 3.893A pdb=" N GLN B 599 " --> pdb=" O ALA B 595 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N THR B 600 " --> pdb=" O CYS B 596 " (cutoff:3.500A) Processing helix chain 'B' and resid 615 through 634 removed outlier: 3.589A pdb=" N SER B 619 " --> pdb=" O HIS B 615 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET B 630 " --> pdb=" O CYS B 626 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N SER B 634 " --> pdb=" O MET B 630 " (cutoff:3.500A) Processing helix chain 'B' and resid 634 through 652 removed outlier: 3.533A pdb=" N LEU B 643 " --> pdb=" O LEU B 639 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LYS B 650 " --> pdb=" O GLY B 646 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA2, first strand: chain 'A' and resid 326 through 329 Processing sheet with id=AA3, first strand: chain 'B' and resid 313 through 314 Processing sheet with id=AA4, first strand: chain 'B' and resid 326 through 329 496 hydrogen bonds defined for protein. 1416 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.24 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 2474 1.35 - 1.47: 2320 1.47 - 1.60: 3728 1.60 - 1.73: 0 1.73 - 1.85: 104 Bond restraints: 8626 Sorted by residual: bond pdb=" C5 GLC F 2 " pdb=" O5 GLC F 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C5 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.415 1.503 -0.088 2.00e-02 2.50e+03 1.94e+01 bond pdb=" C1 BGC E 1 " pdb=" O5 BGC E 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 BGC J 1 " pdb=" O5 BGC J 1 " ideal model delta sigma weight residual 1.408 1.494 -0.086 2.00e-02 2.50e+03 1.85e+01 bond pdb=" C1 GLC I 2 " pdb=" O5 GLC I 2 " ideal model delta sigma weight residual 1.402 1.485 -0.083 2.00e-02 2.50e+03 1.71e+01 ... (remaining 8621 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 11129 2.08 - 4.16: 506 4.16 - 6.24: 123 6.24 - 8.32: 21 8.32 - 10.40: 15 Bond angle restraints: 11794 Sorted by residual: angle pdb=" N VAL A 431 " pdb=" CA VAL A 431 " pdb=" C VAL A 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" N VAL B 431 " pdb=" CA VAL B 431 " pdb=" C VAL B 431 " ideal model delta sigma weight residual 113.42 108.21 5.21 1.17e+00 7.31e-01 1.98e+01 angle pdb=" C PRO B 230 " pdb=" N PRO B 231 " pdb=" CA PRO B 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C PRO A 230 " pdb=" N PRO A 231 " pdb=" CA PRO A 231 " ideal model delta sigma weight residual 120.83 116.57 4.26 1.02e+00 9.61e-01 1.74e+01 angle pdb=" C ILE A 571 " pdb=" N ALA A 572 " pdb=" CA ALA A 572 " ideal model delta sigma weight residual 122.40 128.23 -5.83 1.45e+00 4.76e-01 1.62e+01 ... (remaining 11789 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.22: 5238 34.22 - 68.43: 52 68.43 - 102.65: 42 102.65 - 136.86: 32 136.86 - 171.08: 2 Dihedral angle restraints: 5366 sinusoidal: 2284 harmonic: 3082 Sorted by residual: dihedral pdb=" C26 DU0 A2000 " pdb=" C24 DU0 A2000 " pdb=" C25 DU0 A2000 " pdb=" O23 DU0 A2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C26 DU0 B2000 " pdb=" C24 DU0 B2000 " pdb=" C25 DU0 B2000 " pdb=" O23 DU0 B2000 " ideal model delta sinusoidal sigma weight residual 189.32 18.24 171.08 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" O2 GLC F 2 " pdb=" C2 GLC F 2 " pdb=" C3 GLC F 2 " pdb=" O3 GLC F 2 " ideal model delta sinusoidal sigma weight residual 60.18 -167.16 -132.66 1 3.00e+01 1.11e-03 1.79e+01 ... (remaining 5363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 1252 0.083 - 0.167: 198 0.167 - 0.250: 12 0.250 - 0.333: 2 0.333 - 0.417: 2 Chirality restraints: 1466 Sorted by residual: chirality pdb=" C1 NAG C 1 " pdb=" ND2 ASN A 312 " pdb=" C2 NAG C 1 " pdb=" O5 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C1 NAG G 1 " pdb=" ND2 ASN B 312 " pdb=" C2 NAG G 1 " pdb=" O5 NAG G 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.82 0.42 2.00e-01 2.50e+01 4.34e+00 chirality pdb=" C4 NAG C 1 " pdb=" C3 NAG C 1 " pdb=" C5 NAG C 1 " pdb=" O4 NAG C 1 " both_signs ideal model delta sigma weight residual False -2.53 -2.26 -0.27 2.00e-01 2.50e+01 1.80e+00 ... (remaining 1463 not shown) Planarity restraints: 1408 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU B 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO B 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO B 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO B 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 408 " -0.043 5.00e-02 4.00e+02 6.35e-02 6.45e+00 pdb=" N PRO A 409 " 0.110 5.00e-02 4.00e+02 pdb=" CA PRO A 409 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO A 409 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 473 " 0.011 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE A 473 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 473 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE A 473 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 473 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 473 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE A 473 " -0.000 2.00e-02 2.50e+03 ... (remaining 1405 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.91: 3176 2.91 - 3.46: 9098 3.46 - 4.02: 15205 4.02 - 4.58: 21610 4.58 - 5.14: 31161 Nonbonded interactions: 80250 Sorted by model distance: nonbonded pdb=" O ILE A 169 " pdb=" OG SER A 172 " model vdw 2.348 3.040 nonbonded pdb=" O ILE B 169 " pdb=" OG SER B 172 " model vdw 2.348 3.040 nonbonded pdb=" O2 GLC F 2 " pdb=" O4 GLC F 2 " model vdw 2.383 3.040 nonbonded pdb=" O2 GLC I 2 " pdb=" O4 GLC I 2 " model vdw 2.383 3.040 nonbonded pdb=" O GLU A 222 " pdb=" OG1 THR A 226 " model vdw 2.383 3.040 ... (remaining 80245 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'J' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 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: 0.000 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 22.490 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:10.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.230 ------------------------------------------------------------------------------- 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 8626 Z= 0.566 Angle : 1.123 10.401 11794 Z= 0.597 Chirality : 0.061 0.417 1466 Planarity : 0.007 0.063 1404 Dihedral : 18.504 171.079 3380 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 0.23 % Allowed : 2.38 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.53 (0.20), residues: 1070 helix: -2.09 (0.16), residues: 632 sheet: None (None), residues: 0 loop : -2.58 (0.25), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP A 339 HIS 0.003 0.001 HIS B 394 PHE 0.036 0.004 PHE A 473 TYR 0.027 0.003 TYR B 466 ARG 0.006 0.001 ARG B 528 *********************** 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 : 0.913 Fit side-chains REVERT: A 400 ASP cc_start: 0.8009 (t0) cc_final: 0.7793 (t0) REVERT: A 405 LYS cc_start: 0.8314 (tttp) cc_final: 0.8078 (tttp) REVERT: A 449 LYS cc_start: 0.8156 (tttp) cc_final: 0.7754 (ttmt) REVERT: A 488 ASP cc_start: 0.8046 (m-30) cc_final: 0.7657 (m-30) REVERT: A 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7093 (mtp85) REVERT: B 400 ASP cc_start: 0.7975 (t0) cc_final: 0.7765 (t0) REVERT: B 405 LYS cc_start: 0.8302 (tttp) cc_final: 0.8065 (tttp) REVERT: B 449 LYS cc_start: 0.8152 (tttp) cc_final: 0.7744 (ttmt) REVERT: B 528 ARG cc_start: 0.7315 (mmt-90) cc_final: 0.7098 (mtp85) outliers start: 2 outliers final: 1 residues processed: 244 average time/residue: 1.0795 time to fit residues: 281.4702 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 : 0.906 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 315 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 54 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 83 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 0.7980 chunk 96 optimal weight: 2.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 130 GLN A 131 ASN A 347 ASN A 537 ASN A 615 HIS B 130 GLN B 131 ASN B 347 ASN B 537 ASN B 606 ASN B 615 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.125495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.097854 restraints weight = 9749.171| |-----------------------------------------------------------------------------| r_work (start): 0.3032 rms_B_bonded: 2.05 r_work: 0.2903 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8626 Z= 0.229 Angle : 0.741 11.169 11794 Z= 0.340 Chirality : 0.058 1.003 1466 Planarity : 0.005 0.058 1404 Dihedral : 15.827 145.443 1650 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 3.74 % Allowed : 10.88 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.24), residues: 1070 helix: 0.02 (0.19), residues: 640 sheet: None (None), residues: 0 loop : -2.08 (0.27), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.002 0.001 HIS A 394 PHE 0.011 0.002 PHE B 427 TYR 0.015 0.002 TYR B 292 ARG 0.004 0.001 ARG B 317 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2140 Ramachandran restraints generated. 1070 Oldfield, 0 Emsley, 1070 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 159 time to evaluate : 1.134 Fit side-chains REVERT: A 274 ASN cc_start: 0.8427 (m-40) cc_final: 0.8098 (m110) REVERT: A 400 ASP cc_start: 0.8701 (t0) cc_final: 0.8396 (t0) REVERT: A 528 ARG cc_start: 0.8080 (mmt-90) cc_final: 0.7607 (mtp85) REVERT: A 612 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8099 (ttmp) REVERT: B 274 ASN cc_start: 0.8403 (m-40) cc_final: 0.8061 (m110) REVERT: B 400 ASP cc_start: 0.8672 (t0) cc_final: 0.8363 (t0) REVERT: B 445 ARG cc_start: 0.8018 (mtm110) cc_final: 0.7668 (mtm110) REVERT: B 528 ARG cc_start: 0.8027 (mmt-90) cc_final: 0.7547 (mtp85) REVERT: B 612 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8085 (ttmp) outliers start: 33 outliers final: 15 residues processed: 174 average time/residue: 1.2355 time to fit residues: 228.3837 Evaluate side-chains 156 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 600 THR Chi-restraints excluded: chain A residue 612 LYS Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER Chi-restraints excluded: chain B residue 600 THR Chi-restraints excluded: chain B residue 612 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 20 optimal weight: 8.9990 chunk 21 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.0980 chunk 60 optimal weight: 2.9990 chunk 65 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 70 optimal weight: 0.9990 chunk 80 optimal weight: 0.5980 overall best weight: 0.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 606 ASN B 131 ASN B 606 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.126064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.098124 restraints weight = 9930.055| |-----------------------------------------------------------------------------| r_work (start): 0.3038 rms_B_bonded: 2.08 r_work: 0.2904 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8626 Z= 0.178 Angle : 0.616 6.709 11794 Z= 0.290 Chirality : 0.041 0.175 1466 Planarity : 0.005 0.049 1404 Dihedral : 12.465 145.880 1648 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 4.65 % Allowed : 10.66 % Favored : 84.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.25), residues: 1070 helix: 1.00 (0.20), residues: 640 sheet: None (None), residues: 0 loop : -1.71 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 PHE 0.011 0.001 PHE B 276 TYR 0.011 0.001 TYR A 292 ARG 0.002 0.000 ARG B 317 *********************** 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 190 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 149 time to evaluate : 0.845 Fit side-chains REVERT: A 274 ASN cc_start: 0.8363 (m-40) cc_final: 0.8049 (m110) REVERT: A 400 ASP cc_start: 0.8572 (t0) cc_final: 0.8370 (t0) REVERT: A 496 VAL cc_start: 0.8479 (t) cc_final: 0.8194 (p) REVERT: A 528 ARG cc_start: 0.8163 (mmt-90) cc_final: 0.7699 (mtp85) REVERT: B 274 ASN cc_start: 0.8340 (m-40) cc_final: 0.8023 (m110) REVERT: B 400 ASP cc_start: 0.8530 (t0) cc_final: 0.8330 (t0) REVERT: B 445 ARG cc_start: 0.8016 (mtm110) cc_final: 0.7641 (mtm110) REVERT: B 496 VAL cc_start: 0.8487 (t) cc_final: 0.8211 (p) REVERT: B 528 ARG cc_start: 0.8083 (mmt-90) cc_final: 0.7604 (mtp85) outliers start: 41 outliers final: 17 residues processed: 171 average time/residue: 1.1957 time to fit residues: 217.6422 Evaluate side-chains 157 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 140 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 300 PHE Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain B residue 159 ILE Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 492 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 72 optimal weight: 2.9990 chunk 25 optimal weight: 0.0970 chunk 93 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 29 optimal weight: 4.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 103 optimal weight: 0.0070 chunk 43 optimal weight: 8.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 0.0270 overall best weight: 0.3456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.128783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.100676 restraints weight = 9852.775| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 2.07 r_work: 0.3010 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2874 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2874 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8626 Z= 0.156 Angle : 0.574 7.428 11794 Z= 0.271 Chirality : 0.041 0.177 1466 Planarity : 0.004 0.044 1404 Dihedral : 10.394 141.045 1648 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 4.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.51 % Allowed : 11.45 % Favored : 85.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.26), residues: 1070 helix: 1.61 (0.21), residues: 640 sheet: None (None), residues: 0 loop : -1.51 (0.28), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 501 HIS 0.001 0.000 HIS A 394 PHE 0.012 0.001 PHE A 428 TYR 0.011 0.001 TYR A 216 ARG 0.003 0.000 ARG A 440 *********************** 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 196 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.960 Fit side-chains REVERT: A 274 ASN cc_start: 0.8414 (m-40) cc_final: 0.8127 (m110) REVERT: A 349 THR cc_start: 0.8459 (OUTLIER) cc_final: 0.8156 (p) REVERT: A 440 ARG cc_start: 0.7670 (mtt-85) cc_final: 0.7366 (mtp85) REVERT: A 488 ASP cc_start: 0.8122 (m-30) cc_final: 0.7423 (m-30) REVERT: A 496 VAL cc_start: 0.8570 (t) cc_final: 0.8328 (p) REVERT: A 528 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7745 (mtt90) REVERT: B 274 ASN cc_start: 0.8371 (m-40) cc_final: 0.8088 (m110) REVERT: B 349 THR cc_start: 0.8444 (OUTLIER) cc_final: 0.8122 (p) REVERT: B 440 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7376 (mtp85) REVERT: B 445 ARG cc_start: 0.8006 (mtm110) cc_final: 0.7652 (mtm110) REVERT: B 496 VAL cc_start: 0.8561 (t) cc_final: 0.8328 (p) REVERT: B 528 ARG cc_start: 0.8183 (mmt-90) cc_final: 0.7764 (mtt90) outliers start: 31 outliers final: 14 residues processed: 179 average time/residue: 1.1604 time to fit residues: 221.3684 Evaluate side-chains 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 147 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 82 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 56 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 2 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 28 optimal weight: 5.9990 chunk 67 optimal weight: 0.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 131 ASN A 319 GLN A 377 GLN B 131 ASN B 319 GLN B 377 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.121380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.093370 restraints weight = 9832.818| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 2.06 r_work: 0.2853 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2712 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.3006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8626 Z= 0.289 Angle : 0.645 8.080 11794 Z= 0.308 Chirality : 0.044 0.186 1466 Planarity : 0.004 0.045 1404 Dihedral : 9.723 143.590 1648 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 5.22 % Allowed : 11.68 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.25), residues: 1070 helix: 1.57 (0.20), residues: 642 sheet: None (None), residues: 0 loop : -1.39 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 381 HIS 0.003 0.001 HIS B 394 PHE 0.016 0.002 PHE B 428 TYR 0.017 0.002 TYR B 411 ARG 0.006 0.001 ARG A 191 *********************** 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 201 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 155 time to evaluate : 0.963 Fit side-chains REVERT: A 274 ASN cc_start: 0.8378 (m-40) cc_final: 0.8101 (m110) REVERT: A 301 ASP cc_start: 0.7842 (t0) cc_final: 0.7491 (t0) REVERT: A 349 THR cc_start: 0.8434 (OUTLIER) cc_final: 0.8126 (p) REVERT: A 440 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.7309 (mtp85) REVERT: A 484 ASP cc_start: 0.8060 (OUTLIER) cc_final: 0.7710 (t0) REVERT: A 496 VAL cc_start: 0.8553 (t) cc_final: 0.8322 (p) REVERT: A 528 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7696 (mtp85) REVERT: B 274 ASN cc_start: 0.8361 (m-40) cc_final: 0.8046 (m110) REVERT: B 301 ASP cc_start: 0.7807 (t0) cc_final: 0.7472 (t0) REVERT: B 349 THR cc_start: 0.8411 (OUTLIER) cc_final: 0.8084 (p) REVERT: B 405 LYS cc_start: 0.8020 (tttp) cc_final: 0.7819 (tttp) REVERT: B 440 ARG cc_start: 0.7614 (mtt-85) cc_final: 0.7313 (mtp85) REVERT: B 445 ARG cc_start: 0.7998 (mtm110) cc_final: 0.7746 (mtm110) REVERT: B 484 ASP cc_start: 0.8039 (OUTLIER) cc_final: 0.7705 (t0) REVERT: B 496 VAL cc_start: 0.8529 (t) cc_final: 0.8318 (p) REVERT: B 528 ARG cc_start: 0.8159 (mmt-90) cc_final: 0.7688 (mtp85) outliers start: 46 outliers final: 27 residues processed: 179 average time/residue: 1.1961 time to fit residues: 228.0765 Evaluate side-chains 183 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 152 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 364 GLU Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 418 THR Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 514 SER Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 300 PHE Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 418 THR Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 476 CYS Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 514 SER 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 22 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 71 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 44 optimal weight: 2.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 377 GLN B 319 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.123972 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.096263 restraints weight = 9756.509| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.04 r_work: 0.2956 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2819 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.3162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8626 Z= 0.194 Angle : 0.596 8.775 11794 Z= 0.282 Chirality : 0.042 0.170 1466 Planarity : 0.004 0.042 1404 Dihedral : 8.897 143.805 1648 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 3.97 % Allowed : 15.31 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.26), residues: 1070 helix: 1.93 (0.20), residues: 646 sheet: None (None), residues: 0 loop : -1.33 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 381 HIS 0.001 0.000 HIS A 394 PHE 0.009 0.001 PHE A 428 TYR 0.012 0.001 TYR A 292 ARG 0.005 0.000 ARG B 191 *********************** 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 189 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 0.973 Fit side-chains REVERT: A 274 ASN cc_start: 0.8374 (m-40) cc_final: 0.8086 (m110) REVERT: A 301 ASP cc_start: 0.7823 (t0) cc_final: 0.7478 (t0) REVERT: A 349 THR cc_start: 0.8403 (OUTLIER) cc_final: 0.8093 (p) REVERT: A 440 ARG cc_start: 0.7512 (mtt-85) cc_final: 0.7135 (mtp85) REVERT: A 484 ASP cc_start: 0.8001 (OUTLIER) cc_final: 0.7602 (t0) REVERT: A 496 VAL cc_start: 0.8587 (t) cc_final: 0.8368 (p) REVERT: A 528 ARG cc_start: 0.8170 (mmt-90) cc_final: 0.7795 (mtt180) REVERT: A 647 MET cc_start: 0.6303 (OUTLIER) cc_final: 0.5783 (mtp) REVERT: B 274 ASN cc_start: 0.8363 (m-40) cc_final: 0.8073 (m110) REVERT: B 301 ASP cc_start: 0.7824 (t0) cc_final: 0.7483 (t0) REVERT: B 349 THR cc_start: 0.8387 (OUTLIER) cc_final: 0.8055 (p) REVERT: B 440 ARG cc_start: 0.7521 (mtt-85) cc_final: 0.7160 (mtp85) REVERT: B 445 ARG cc_start: 0.7969 (mtm110) cc_final: 0.7707 (mtm110) REVERT: B 484 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7550 (t0) REVERT: B 496 VAL cc_start: 0.8578 (t) cc_final: 0.8377 (p) REVERT: B 521 GLN cc_start: 0.8383 (OUTLIER) cc_final: 0.8161 (mp10) REVERT: B 528 ARG cc_start: 0.8165 (mmt-90) cc_final: 0.7800 (mtt180) outliers start: 35 outliers final: 18 residues processed: 172 average time/residue: 1.2609 time to fit residues: 230.2583 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 146 time to evaluate : 1.050 ------------------------------------------------------------------------------- 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 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 647 MET Chi-restraints excluded: chain B residue 131 ASN Chi-restraints excluded: chain B residue 179 VAL Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 408 LEU Chi-restraints excluded: chain B residue 434 ILE Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain B residue 492 ARG Chi-restraints excluded: chain B residue 521 GLN Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 102 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 76 optimal weight: 9.9990 chunk 97 optimal weight: 0.6980 chunk 82 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 14 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.6980 chunk 77 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 GLN A 377 GLN B 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 = 0.124253 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.096286 restraints weight = 9967.708| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 2.08 r_work: 0.2943 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2805 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.3255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8626 Z= 0.192 Angle : 0.584 7.442 11794 Z= 0.278 Chirality : 0.041 0.164 1466 Planarity : 0.004 0.042 1404 Dihedral : 7.822 141.530 1648 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.08 % Allowed : 15.65 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.26), residues: 1070 helix: 2.03 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 381 HIS 0.001 0.000 HIS B 547 PHE 0.010 0.001 PHE B 428 TYR 0.012 0.001 TYR A 216 ARG 0.006 0.000 ARG A 445 *********************** 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 184 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 148 time to evaluate : 0.926 Fit side-chains REVERT: A 274 ASN cc_start: 0.8402 (m-40) cc_final: 0.8131 (m110) REVERT: A 301 ASP cc_start: 0.7802 (t0) cc_final: 0.7449 (t0) REVERT: A 349 THR cc_start: 0.8443 (OUTLIER) cc_final: 0.8142 (p) REVERT: A 440 ARG cc_start: 0.7389 (mtt-85) cc_final: 0.7013 (mtp180) REVERT: A 484 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7564 (t0) REVERT: A 496 VAL cc_start: 0.8584 (OUTLIER) cc_final: 0.8380 (p) REVERT: A 528 ARG cc_start: 0.8164 (mmt-90) cc_final: 0.7788 (mtt180) REVERT: A 647 MET cc_start: 0.6266 (OUTLIER) cc_final: 0.5734 (mtp) REVERT: B 274 ASN cc_start: 0.8382 (m-40) cc_final: 0.8099 (m110) REVERT: B 301 ASP cc_start: 0.7808 (t0) cc_final: 0.7462 (t0) REVERT: B 349 THR cc_start: 0.8380 (OUTLIER) cc_final: 0.8045 (p) REVERT: B 440 ARG cc_start: 0.7407 (mtt-85) cc_final: 0.7043 (mtp85) REVERT: B 445 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7649 (mtm110) REVERT: B 484 ASP cc_start: 0.7930 (OUTLIER) cc_final: 0.7537 (t0) REVERT: B 528 ARG cc_start: 0.8157 (mmt-90) cc_final: 0.7774 (mtt180) outliers start: 36 outliers final: 18 residues processed: 166 average time/residue: 1.2298 time to fit residues: 217.0616 Evaluate side-chains 167 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 143 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 179 VAL Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 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 601 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 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 601 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 93 optimal weight: 1.9990 chunk 89 optimal weight: 4.9990 chunk 24 optimal weight: 0.8980 chunk 88 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 73 optimal weight: 7.9990 chunk 15 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3377 r_free = 0.3377 target = 0.124538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.096572 restraints weight = 9952.772| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.08 r_work: 0.2945 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2809 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.3354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 8626 Z= 0.196 Angle : 0.576 6.138 11794 Z= 0.279 Chirality : 0.041 0.165 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.317 139.545 1648 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.51 % Allowed : 16.44 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.26), residues: 1070 helix: 2.14 (0.20), residues: 658 sheet: None (None), residues: 0 loop : -1.14 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 PHE 0.010 0.001 PHE A 428 TYR 0.012 0.001 TYR B 292 ARG 0.004 0.000 ARG B 191 *********************** 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 176 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 145 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8396 (m-40) cc_final: 0.8115 (m110) REVERT: A 301 ASP cc_start: 0.7788 (t0) cc_final: 0.7440 (t0) REVERT: A 349 THR cc_start: 0.8348 (OUTLIER) cc_final: 0.8029 (p) REVERT: A 440 ARG cc_start: 0.7400 (mtt-85) cc_final: 0.7023 (mtp180) REVERT: A 484 ASP cc_start: 0.7915 (OUTLIER) cc_final: 0.7540 (t0) REVERT: A 496 VAL cc_start: 0.8577 (OUTLIER) cc_final: 0.8372 (p) REVERT: A 528 ARG cc_start: 0.8151 (mmt-90) cc_final: 0.7785 (mtt180) REVERT: A 647 MET cc_start: 0.6262 (OUTLIER) cc_final: 0.5729 (mtp) REVERT: B 274 ASN cc_start: 0.8359 (m-40) cc_final: 0.8071 (m110) REVERT: B 301 ASP cc_start: 0.7799 (t0) cc_final: 0.7456 (t0) REVERT: B 349 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8040 (p) REVERT: B 445 ARG cc_start: 0.7961 (mtm110) cc_final: 0.7627 (mtm110) REVERT: B 484 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7519 (t0) REVERT: B 528 ARG cc_start: 0.8142 (mmt-90) cc_final: 0.7772 (mtt180) outliers start: 31 outliers final: 20 residues processed: 162 average time/residue: 1.3010 time to fit residues: 223.3774 Evaluate side-chains 170 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 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 587 MET Chi-restraints excluded: chain A residue 601 LEU Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain B residue 131 ASN 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 601 LEU Chi-restraints excluded: chain B residue 621 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 66 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 56 optimal weight: 3.9990 chunk 95 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 85 optimal weight: 0.0980 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.125845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.098026 restraints weight = 10014.457| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 2.07 r_work: 0.2925 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8626 Z= 0.171 Angle : 0.550 5.994 11794 Z= 0.269 Chirality : 0.040 0.154 1466 Planarity : 0.004 0.041 1404 Dihedral : 7.023 136.048 1648 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.63 % Allowed : 16.67 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.26), residues: 1070 helix: 2.28 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -1.09 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE B 428 TYR 0.013 0.001 TYR A 216 ARG 0.008 0.000 ARG B 191 *********************** 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 180 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 274 ASN cc_start: 0.8329 (m-40) cc_final: 0.8050 (m110) REVERT: A 301 ASP cc_start: 0.7810 (t0) cc_final: 0.7371 (t0) REVERT: A 349 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8010 (p) REVERT: A 484 ASP cc_start: 0.7859 (OUTLIER) cc_final: 0.7471 (t0) REVERT: A 528 ARG cc_start: 0.8125 (mmt-90) cc_final: 0.7733 (mtt180) REVERT: A 647 MET cc_start: 0.6242 (OUTLIER) cc_final: 0.5694 (mtp) REVERT: B 274 ASN cc_start: 0.8306 (m-40) cc_final: 0.8028 (m110) REVERT: B 301 ASP cc_start: 0.7835 (t0) cc_final: 0.7467 (t0) REVERT: B 349 THR cc_start: 0.8377 (OUTLIER) cc_final: 0.8078 (p) REVERT: B 440 ARG cc_start: 0.7905 (mtp85) cc_final: 0.7369 (mtp85) REVERT: B 445 ARG cc_start: 0.7941 (mtm110) cc_final: 0.7598 (mtm110) REVERT: B 484 ASP cc_start: 0.7808 (OUTLIER) cc_final: 0.7421 (t0) REVERT: B 521 GLN cc_start: 0.8472 (OUTLIER) cc_final: 0.8056 (mp10) REVERT: B 528 ARG cc_start: 0.8135 (mmt-90) cc_final: 0.7757 (mtt180) outliers start: 32 outliers final: 17 residues processed: 165 average time/residue: 1.2825 time to fit residues: 224.4554 Evaluate side-chains 164 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 141 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 647 MET Chi-restraints excluded: chain B residue 185 SER Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain B residue 298 SER Chi-restraints excluded: chain B residue 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 521 GLN Chi-restraints excluded: chain B residue 601 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 98 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 0.5980 chunk 63 optimal weight: 1.9990 chunk 49 optimal weight: 0.0040 chunk 18 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.3401 r_free = 0.3401 target = 0.126418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.098582 restraints weight = 9948.918| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.06 r_work: 0.2982 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8626 Z= 0.166 Angle : 0.556 5.863 11794 Z= 0.272 Chirality : 0.040 0.154 1466 Planarity : 0.004 0.050 1404 Dihedral : 6.835 134.617 1648 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 2.61 % Allowed : 17.23 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.27), residues: 1070 helix: 2.39 (0.20), residues: 660 sheet: None (None), residues: 0 loop : -0.96 (0.31), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 381 HIS 0.001 0.000 HIS A 547 PHE 0.009 0.001 PHE A 428 TYR 0.015 0.001 TYR B 613 ARG 0.011 0.001 ARG A 445 ********************** 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 163 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 140 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 131 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8579 (m-40) REVERT: A 274 ASN cc_start: 0.8339 (m-40) cc_final: 0.8046 (m110) REVERT: A 301 ASP cc_start: 0.7781 (t0) cc_final: 0.7349 (t0) REVERT: A 349 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.7990 (p) REVERT: A 440 ARG cc_start: 0.7980 (mtp85) cc_final: 0.7450 (mmm-85) REVERT: A 484 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7445 (t0) REVERT: A 528 ARG cc_start: 0.8124 (mmt-90) cc_final: 0.7755 (mtt180) REVERT: A 647 MET cc_start: 0.6284 (OUTLIER) cc_final: 0.5719 (mtp) REVERT: B 274 ASN cc_start: 0.8313 (m-40) cc_final: 0.8028 (m110) REVERT: B 301 ASP cc_start: 0.7821 (t0) cc_final: 0.7467 (t0) REVERT: B 349 THR cc_start: 0.8317 (OUTLIER) cc_final: 0.7979 (p) REVERT: B 445 ARG cc_start: 0.7929 (mtm110) cc_final: 0.7588 (mtm110) REVERT: B 484 ASP cc_start: 0.7745 (OUTLIER) cc_final: 0.7366 (t0) REVERT: B 528 ARG cc_start: 0.8161 (mmt-90) cc_final: 0.7793 (mtt180) outliers start: 23 outliers final: 14 residues processed: 153 average time/residue: 1.3577 time to fit residues: 220.4222 Evaluate side-chains 161 residues out of total 882 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 141 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 ASN Chi-restraints excluded: chain A residue 159 ILE Chi-restraints excluded: chain A residue 270 VAL Chi-restraints excluded: chain A residue 290 SER Chi-restraints excluded: chain A residue 298 SER Chi-restraints excluded: chain A residue 322 ILE Chi-restraints excluded: chain A residue 349 THR Chi-restraints excluded: chain A residue 408 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain A residue 492 ARG Chi-restraints excluded: chain A residue 647 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.0050 chunk 46 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- 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 = 0.3403 r_free = 0.3403 target = 0.126519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.098558 restraints weight = 10098.655| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.08 r_work: 0.2986 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2852 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8626 Z= 0.162 Angle : 0.544 5.781 11794 Z= 0.267 Chirality : 0.040 0.151 1466 Planarity : 0.004 0.040 1404 Dihedral : 6.702 133.219 1648 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.49 % Allowed : 17.35 % Favored : 80.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 1070 helix: 2.44 (0.20), residues: 664 sheet: None (None), residues: 0 loop : -0.97 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 381 HIS 0.001 0.000 HIS B 547 PHE 0.009 0.001 PHE B 428 TYR 0.011 0.001 TYR A 292 ARG 0.007 0.001 ARG A 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6223.63 seconds wall clock time: 110 minutes 39.13 seconds (6639.13 seconds total)