Starting phenix.real_space_refine on Sun May 3 23:45:27 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.cif Found real_map, /net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.map" model { file = "/net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9efs_47978/05_2026/9efs_47978.cif" } resolution = 2.6 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= 0.001 sd= 0.043 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: 4 Type Number sf(0) Gaussians S 81 5.16 5 C 10242 2.51 5 N 2820 2.21 5 O 3000 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16143 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5353 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 4 Chain: "B" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5353 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 4 Chain: "C" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 673, 5353 Classifications: {'peptide': 673} Link IDs: {'PTRANS': 29, 'TRANS': 643} Chain breaks: 4 Chain: "A" 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: "B" 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: "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 Time building chain proxies: 3.94, per 1000 atoms: 0.24 Number of scatterers: 16143 At special positions: 0 Unit cell: (122.76, 116.16, 170.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 81 16.00 O 3000 8.00 N 2820 7.00 C 10242 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 116 " - pdb=" SG CYS A 573 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 529 " distance=2.03 Simple disulfide: pdb=" SG CYS A 207 " - pdb=" SG CYS A 271 " distance=2.03 Simple disulfide: pdb=" SG CYS A 364 " - pdb=" SG CYS A 412 " distance=2.03 Simple disulfide: pdb=" SG CYS A 596 " - pdb=" SG CYS A 633 " distance=2.04 Simple disulfide: pdb=" SG CYS B 116 " - pdb=" SG CYS B 573 " distance=2.03 Simple disulfide: pdb=" SG CYS B 133 " - pdb=" SG CYS B 529 " distance=2.03 Simple disulfide: pdb=" SG CYS B 207 " - pdb=" SG CYS B 271 " distance=2.03 Simple disulfide: pdb=" SG CYS B 364 " - pdb=" SG CYS B 412 " distance=2.03 Simple disulfide: pdb=" SG CYS B 596 " - pdb=" SG CYS B 633 " distance=2.04 Simple disulfide: pdb=" SG CYS C 116 " - pdb=" SG CYS C 573 " distance=2.03 Simple disulfide: pdb=" SG CYS C 133 " - pdb=" SG CYS C 529 " distance=2.03 Simple disulfide: pdb=" SG CYS C 207 " - pdb=" SG CYS C 271 " distance=2.03 Simple disulfide: pdb=" SG CYS C 364 " - pdb=" SG CYS C 412 " distance=2.03 Simple disulfide: pdb=" SG CYS C 596 " - pdb=" SG CYS C 633 " distance=2.04 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=0, symmetry=0 Links applied NAG-ASN " NAG A1001 " - " ASN A 141 " " NAG A1002 " - " ASN A 398 " " NAG B1001 " - " ASN B 141 " " NAG B1002 " - " ASN B 398 " " NAG C1001 " - " ASN C 141 " " NAG C1002 " - " ASN C 398 " Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 777.5 milliseconds 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3780 Finding SS restraints... Secondary structure from input PDB file: 58 helices and 33 sheets defined 36.3% alpha, 27.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 91 through 105 removed outlier: 3.814A pdb=" N ALA A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 225 through 227 No H-bonds generated for 'chain 'A' and resid 225 through 227' Processing helix chain 'A' and resid 260 through 265 Processing helix chain 'A' and resid 306 through 310 removed outlier: 3.651A pdb=" N GLU A 310 " --> pdb=" O SER A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 317 No H-bonds generated for 'chain 'A' and resid 315 through 317' Processing helix chain 'A' and resid 403 through 409 Processing helix chain 'A' and resid 413 through 428 Processing helix chain 'A' and resid 458 through 468 Processing helix chain 'A' and resid 510 through 546 removed outlier: 4.635A pdb=" N HIS A 516 " --> pdb=" O HIS A 512 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 517 " --> pdb=" O ILE A 513 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VAL A 524 " --> pdb=" O MET A 520 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 577 through 579 No H-bonds generated for 'chain 'A' and resid 577 through 579' Processing helix chain 'A' and resid 669 through 675 removed outlier: 4.059A pdb=" N ILE A 675 " --> pdb=" O ILE A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 691 Processing helix chain 'A' and resid 701 through 724 Processing helix chain 'A' and resid 726 through 739 removed outlier: 4.254A pdb=" N ALA A 730 " --> pdb=" O ASP A 726 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N MET A 731 " --> pdb=" O ALA A 727 " (cutoff:3.500A) Processing helix chain 'A' and resid 747 through 773 removed outlier: 3.729A pdb=" N ASN A 773 " --> pdb=" O SER A 769 " (cutoff:3.500A) Processing helix chain 'A' and resid 773 through 803 removed outlier: 3.596A pdb=" N SER A 803 " --> pdb=" O MET A 799 " (cutoff:3.500A) Processing helix chain 'A' and resid 804 through 810 Processing helix chain 'B' and resid 92 through 105 Processing helix chain 'B' and resid 193 through 200 Processing helix chain 'B' and resid 225 through 227 No H-bonds generated for 'chain 'B' and resid 225 through 227' Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 306 through 310 removed outlier: 3.654A pdb=" N GLU B 310 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 315 through 317 No H-bonds generated for 'chain 'B' and resid 315 through 317' Processing helix chain 'B' and resid 403 through 408 removed outlier: 3.501A pdb=" N VAL B 407 " --> pdb=" O PRO B 403 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 428 removed outlier: 4.001A pdb=" N ASP B 416 " --> pdb=" O CYS B 412 " (cutoff:3.500A) Processing helix chain 'B' and resid 458 through 468 Processing helix chain 'B' and resid 510 through 546 removed outlier: 4.622A pdb=" N HIS B 516 " --> pdb=" O HIS B 512 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N VAL B 517 " --> pdb=" O ILE B 513 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N VAL B 524 " --> pdb=" O MET B 520 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 577 through 579 No H-bonds generated for 'chain 'B' and resid 577 through 579' Processing helix chain 'B' and resid 669 through 675 removed outlier: 4.104A pdb=" N ILE B 675 " --> pdb=" O ILE B 671 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 691 Processing helix chain 'B' and resid 701 through 724 Processing helix chain 'B' and resid 726 through 739 removed outlier: 4.260A pdb=" N ALA B 730 " --> pdb=" O ASP B 726 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET B 731 " --> pdb=" O ALA B 727 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 773 removed outlier: 3.707A pdb=" N ASN B 773 " --> pdb=" O SER B 769 " (cutoff:3.500A) Processing helix chain 'B' and resid 773 through 803 removed outlier: 3.614A pdb=" N SER B 803 " --> pdb=" O MET B 799 " (cutoff:3.500A) Processing helix chain 'B' and resid 804 through 810 Processing helix chain 'C' and resid 92 through 105 Processing helix chain 'C' and resid 179 through 183 Processing helix chain 'C' and resid 193 through 205 removed outlier: 4.003A pdb=" N ASN C 202 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N ALA C 203 " --> pdb=" O ASP C 199 " (cutoff:3.500A) Processing helix chain 'C' and resid 225 through 227 No H-bonds generated for 'chain 'C' and resid 225 through 227' Processing helix chain 'C' and resid 260 through 265 Processing helix chain 'C' and resid 306 through 310 Processing helix chain 'C' and resid 315 through 317 No H-bonds generated for 'chain 'C' and resid 315 through 317' Processing helix chain 'C' and resid 403 through 408 Processing helix chain 'C' and resid 411 through 428 removed outlier: 3.953A pdb=" N ASP C 416 " --> pdb=" O CYS C 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 468 Processing helix chain 'C' and resid 510 through 546 removed outlier: 4.795A pdb=" N HIS C 516 " --> pdb=" O HIS C 512 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N VAL C 517 " --> pdb=" O ILE C 513 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N VAL C 524 " --> pdb=" O MET C 520 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 577 through 579 No H-bonds generated for 'chain 'C' and resid 577 through 579' Processing helix chain 'C' and resid 670 through 675 Processing helix chain 'C' and resid 686 through 691 Processing helix chain 'C' and resid 701 through 724 Processing helix chain 'C' and resid 726 through 739 removed outlier: 4.259A pdb=" N ALA C 730 " --> pdb=" O ASP C 726 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N MET C 731 " --> pdb=" O ALA C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 773 removed outlier: 3.732A pdb=" N ASN C 773 " --> pdb=" O SER C 769 " (cutoff:3.500A) Processing helix chain 'C' and resid 773 through 803 removed outlier: 3.585A pdb=" N SER C 803 " --> pdb=" O MET C 799 " (cutoff:3.500A) Processing helix chain 'C' and resid 804 through 810 Processing sheet with id=AA1, first strand: chain 'A' and resid 113 through 115 Processing sheet with id=AA2, first strand: chain 'A' and resid 559 through 563 removed outlier: 3.833A pdb=" N THR B 665 " --> pdb=" O VAL A 124 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 152 removed outlier: 6.298A pdb=" N THR A 143 " --> pdb=" O MET A 375 " (cutoff:3.500A) removed outlier: 6.081A pdb=" N MET A 375 " --> pdb=" O THR A 143 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N GLY A 145 " --> pdb=" O ASP A 373 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N ASP A 373 " --> pdb=" O GLY A 145 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N ALA A 147 " --> pdb=" O GLU A 371 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N GLU A 371 " --> pdb=" O ALA A 147 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N VAL A 149 " --> pdb=" O TRP A 369 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N ASN A 398 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LEU A 443 " --> pdb=" O ASN A 398 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N PHE A 448 " --> pdb=" O ALA A 444 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 186 through 191 Processing sheet with id=AA5, first strand: chain 'A' and resid 235 through 236 removed outlier: 7.445A pdb=" N LYS A 160 " --> pdb=" O ASP A 355 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASP A 355 " --> pdb=" O LYS A 160 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 206 through 208 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 Processing sheet with id=AA8, first strand: chain 'A' and resid 433 through 435 Processing sheet with id=AA9, first strand: chain 'A' and resid 581 through 583 Processing sheet with id=AB1, first strand: chain 'A' and resid 595 through 597 Processing sheet with id=AB2, first strand: chain 'A' and resid 638 through 643 removed outlier: 3.562A pdb=" N HIS A 657 " --> pdb=" O TYR A 649 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N GLU A 651 " --> pdb=" O TYR A 655 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N TYR A 655 " --> pdb=" O GLU A 651 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 665 through 666 removed outlier: 6.313A pdb=" N THR A 665 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 113 through 115 Processing sheet with id=AB5, first strand: chain 'B' and resid 559 through 563 removed outlier: 3.873A pdb=" N THR C 665 " --> pdb=" O VAL B 124 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 143 through 152 removed outlier: 6.321A pdb=" N THR B 143 " --> pdb=" O MET B 375 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N MET B 375 " --> pdb=" O THR B 143 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY B 145 " --> pdb=" O ASP B 373 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N ASP B 373 " --> pdb=" O GLY B 145 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ALA B 147 " --> pdb=" O GLU B 371 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU B 371 " --> pdb=" O ALA B 147 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N VAL B 149 " --> pdb=" O TRP B 369 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N ASN B 398 " --> pdb=" O LEU B 443 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N LEU B 443 " --> pdb=" O ASN B 398 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE B 448 " --> pdb=" O ALA B 444 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 186 through 191 Processing sheet with id=AB8, first strand: chain 'B' and resid 235 through 236 removed outlier: 7.403A pdb=" N LYS B 160 " --> pdb=" O ASP B 355 " (cutoff:3.500A) removed outlier: 4.954A pdb=" N ASP B 355 " --> pdb=" O LYS B 160 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 206 through 208 Processing sheet with id=AC1, first strand: chain 'B' and resid 210 through 215 Processing sheet with id=AC2, first strand: chain 'B' and resid 433 through 435 Processing sheet with id=AC3, first strand: chain 'B' and resid 581 through 583 Processing sheet with id=AC4, first strand: chain 'B' and resid 595 through 597 Processing sheet with id=AC5, first strand: chain 'B' and resid 638 through 643 removed outlier: 3.558A pdb=" N HIS B 657 " --> pdb=" O TYR B 649 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N GLU B 651 " --> pdb=" O TYR B 655 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N TYR B 655 " --> pdb=" O GLU B 651 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'C' and resid 113 through 115 Processing sheet with id=AC7, first strand: chain 'C' and resid 144 through 152 removed outlier: 6.430A pdb=" N GLY C 145 " --> pdb=" O ASP C 373 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ASP C 373 " --> pdb=" O GLY C 145 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA C 147 " --> pdb=" O GLU C 371 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N GLU C 371 " --> pdb=" O ALA C 147 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N VAL C 149 " --> pdb=" O TRP C 369 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N ASN C 398 " --> pdb=" O LEU C 443 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LEU C 443 " --> pdb=" O ASN C 398 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE C 448 " --> pdb=" O ALA C 444 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 186 through 191 Processing sheet with id=AC9, first strand: chain 'C' and resid 235 through 236 removed outlier: 7.425A pdb=" N LYS C 160 " --> pdb=" O ASP C 355 " (cutoff:3.500A) removed outlier: 4.953A pdb=" N ASP C 355 " --> pdb=" O LYS C 160 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 206 through 208 Processing sheet with id=AD2, first strand: chain 'C' and resid 210 through 215 Processing sheet with id=AD3, first strand: chain 'C' and resid 433 through 435 Processing sheet with id=AD4, first strand: chain 'C' and resid 581 through 583 Processing sheet with id=AD5, first strand: chain 'C' and resid 595 through 597 Processing sheet with id=AD6, first strand: chain 'C' and resid 638 through 643 removed outlier: 3.551A pdb=" N HIS C 657 " --> pdb=" O TYR C 649 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N GLU C 651 " --> pdb=" O TYR C 655 " (cutoff:3.500A) removed outlier: 5.221A pdb=" N TYR C 655 " --> pdb=" O GLU C 651 " (cutoff:3.500A) 831 hydrogen bonds defined for protein. 2328 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: 3.13 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5331 1.34 - 1.46: 4144 1.46 - 1.59: 6929 1.59 - 1.71: 0 1.71 - 1.83: 132 Bond restraints: 16536 Sorted by residual: bond pdb=" CA GLY B 565 " pdb=" C GLY B 565 " ideal model delta sigma weight residual 1.530 1.512 0.018 1.04e-02 9.25e+03 3.11e+00 bond pdb=" N GLY B 565 " pdb=" CA GLY B 565 " ideal model delta sigma weight residual 1.464 1.446 0.018 1.12e-02 7.97e+03 2.62e+00 bond pdb=" CG1 ILE C 526 " pdb=" CD1 ILE C 526 " ideal model delta sigma weight residual 1.513 1.461 0.052 3.90e-02 6.57e+02 1.78e+00 bond pdb=" CA ASP C 167 " pdb=" CB ASP C 167 " ideal model delta sigma weight residual 1.530 1.550 -0.020 1.55e-02 4.16e+03 1.63e+00 bond pdb=" CG1 ILE B 526 " pdb=" CD1 ILE B 526 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.56e+00 ... (remaining 16531 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 22138 1.86 - 3.73: 288 3.73 - 5.59: 17 5.59 - 7.45: 3 7.45 - 9.32: 3 Bond angle restraints: 22449 Sorted by residual: angle pdb=" C ASP C 167 " pdb=" CA ASP C 167 " pdb=" CB ASP C 167 " ideal model delta sigma weight residual 109.48 114.77 -5.29 1.68e+00 3.54e-01 9.92e+00 angle pdb=" N ILE B 723 " pdb=" CA ILE B 723 " pdb=" C ILE B 723 " ideal model delta sigma weight residual 110.53 113.36 -2.83 9.40e-01 1.13e+00 9.04e+00 angle pdb=" N ALA C 390 " pdb=" CA ALA C 390 " pdb=" C ALA C 390 " ideal model delta sigma weight residual 113.55 109.84 3.71 1.26e+00 6.30e-01 8.66e+00 angle pdb=" N ILE A 723 " pdb=" CA ILE A 723 " pdb=" C ILE A 723 " ideal model delta sigma weight residual 110.53 113.27 -2.74 9.40e-01 1.13e+00 8.47e+00 angle pdb=" C ASP B 167 " pdb=" CA ASP B 167 " pdb=" CB ASP B 167 " ideal model delta sigma weight residual 109.38 114.54 -5.16 1.80e+00 3.09e-01 8.21e+00 ... (remaining 22444 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 8612 17.89 - 35.77: 925 35.77 - 53.66: 253 53.66 - 71.55: 64 71.55 - 89.44: 13 Dihedral angle restraints: 9867 sinusoidal: 3981 harmonic: 5886 Sorted by residual: dihedral pdb=" CB CYS B 133 " pdb=" SG CYS B 133 " pdb=" SG CYS B 529 " pdb=" CB CYS B 529 " ideal model delta sinusoidal sigma weight residual -86.00 -166.87 80.87 1 1.00e+01 1.00e-02 8.08e+01 dihedral pdb=" CB CYS A 133 " pdb=" SG CYS A 133 " pdb=" SG CYS A 529 " pdb=" CB CYS A 529 " ideal model delta sinusoidal sigma weight residual -86.00 -165.53 79.53 1 1.00e+01 1.00e-02 7.86e+01 dihedral pdb=" CB CYS C 133 " pdb=" SG CYS C 133 " pdb=" SG CYS C 529 " pdb=" CB CYS C 529 " ideal model delta sinusoidal sigma weight residual -86.00 -164.98 78.98 1 1.00e+01 1.00e-02 7.76e+01 ... (remaining 9864 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 2190 0.063 - 0.126: 269 0.126 - 0.189: 7 0.189 - 0.251: 2 0.251 - 0.314: 1 Chirality restraints: 2469 Sorted by residual: chirality pdb=" C1 NAG C1001 " pdb=" ND2 ASN C 141 " pdb=" C2 NAG C1001 " pdb=" O5 NAG C1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.09 -0.31 2.00e-01 2.50e+01 2.47e+00 chirality pdb=" C1 NAG B1001 " pdb=" ND2 ASN B 141 " pdb=" C2 NAG B1001 " pdb=" O5 NAG B1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" C1 NAG A1001 " pdb=" ND2 ASN A 141 " pdb=" C2 NAG A1001 " pdb=" O5 NAG A1001 " both_signs ideal model delta sigma weight residual False -2.40 -2.18 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2466 not shown) Planarity restraints: 2919 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 301 " -0.005 2.00e-02 2.50e+03 1.02e-02 2.10e+00 pdb=" CG TYR B 301 " 0.024 2.00e-02 2.50e+03 pdb=" CD1 TYR B 301 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR B 301 " -0.011 2.00e-02 2.50e+03 pdb=" CE1 TYR B 301 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 301 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR B 301 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 301 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 167 " 0.007 2.00e-02 2.50e+03 1.45e-02 2.10e+00 pdb=" C ASP C 167 " -0.025 2.00e-02 2.50e+03 pdb=" O ASP C 167 " 0.009 2.00e-02 2.50e+03 pdb=" N VAL C 168 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 167 " -0.007 2.00e-02 2.50e+03 1.36e-02 1.85e+00 pdb=" C ASP B 167 " 0.023 2.00e-02 2.50e+03 pdb=" O ASP B 167 " -0.009 2.00e-02 2.50e+03 pdb=" N VAL B 168 " -0.008 2.00e-02 2.50e+03 ... (remaining 2916 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 3544 2.78 - 3.31: 13904 3.31 - 3.84: 26477 3.84 - 4.37: 31045 4.37 - 4.90: 54581 Nonbonded interactions: 129551 Sorted by model distance: nonbonded pdb=" O GLN A 172 " pdb=" OG SER A 180 " model vdw 2.254 3.040 nonbonded pdb=" O GLN B 172 " pdb=" OG SER B 180 " model vdw 2.257 3.040 nonbonded pdb=" NH2 ARG B 558 " pdb=" O ASN B 620 " model vdw 2.262 3.120 nonbonded pdb=" O SER A 313 " pdb=" OG SER A 313 " model vdw 2.262 3.040 nonbonded pdb=" NH2 ARG C 558 " pdb=" O ASN C 620 " model vdw 2.286 3.120 ... (remaining 129546 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' selection = chain 'C' } 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: 10.530 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: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.030 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 16557 Z= 0.143 Angle : 0.549 9.319 22497 Z= 0.313 Chirality : 0.040 0.314 2469 Planarity : 0.004 0.053 2913 Dihedral : 16.033 89.437 6042 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.77 % Allowed : 22.18 % Favored : 75.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.19), residues: 1989 helix: 2.68 (0.21), residues: 645 sheet: 0.68 (0.24), residues: 468 loop : -0.60 (0.19), residues: 876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 264 TYR 0.024 0.001 TYR B 301 PHE 0.018 0.001 PHE A 795 TRP 0.009 0.001 TRP C 528 HIS 0.005 0.001 HIS B 263 Details of bonding type rmsd covalent geometry : bond 0.00295 (16536) covalent geometry : angle 0.54401 (22449) SS BOND : bond 0.00296 ( 15) SS BOND : angle 1.26660 ( 30) hydrogen bonds : bond 0.14094 ( 789) hydrogen bonds : angle 6.33688 ( 2328) link_NAG-ASN : bond 0.00481 ( 6) link_NAG-ASN : angle 2.29958 ( 18) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.613 Fit side-chains REVERT: A 297 MET cc_start: 0.8726 (OUTLIER) cc_final: 0.8521 (ttp) REVERT: A 320 LYS cc_start: 0.8298 (tttp) cc_final: 0.8048 (ttmt) REVERT: A 374 GLU cc_start: 0.8245 (pt0) cc_final: 0.7031 (tp30) REVERT: A 607 GLU cc_start: 0.7393 (OUTLIER) cc_final: 0.7020 (mt-10) REVERT: B 144 GLU cc_start: 0.7738 (pt0) cc_final: 0.6320 (tp30) REVERT: B 204 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.7762 (mtmm) REVERT: B 320 LYS cc_start: 0.8364 (tttp) cc_final: 0.7971 (ttmt) REVERT: B 349 LYS cc_start: 0.8163 (ptmt) cc_final: 0.7725 (ttpt) REVERT: B 505 ARG cc_start: 0.5514 (OUTLIER) cc_final: 0.5153 (pmt170) REVERT: B 530 GLU cc_start: 0.7981 (pt0) cc_final: 0.7594 (mt-10) REVERT: C 144 GLU cc_start: 0.7813 (pt0) cc_final: 0.6290 (tp30) REVERT: C 320 LYS cc_start: 0.8441 (tttp) cc_final: 0.8056 (ttmt) REVERT: C 349 LYS cc_start: 0.8190 (ptmt) cc_final: 0.7737 (ttpt) REVERT: C 375 MET cc_start: 0.8456 (ttt) cc_final: 0.8208 (tpp) REVERT: C 530 GLU cc_start: 0.7747 (pt0) cc_final: 0.7434 (mt-10) REVERT: C 642 THR cc_start: 0.8968 (OUTLIER) cc_final: 0.8635 (m) REVERT: C 768 SER cc_start: 0.7870 (t) cc_final: 0.7187 (m) outliers start: 47 outliers final: 33 residues processed: 235 average time/residue: 0.5037 time to fit residues: 133.3617 Evaluate side-chains 227 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 189 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 297 MET Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 362 SER Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 607 GLU Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain B residue 204 LYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 235 LYS Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 362 SER Chi-restraints excluded: chain B residue 372 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 362 SER Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 590 SER Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 10.0000 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 3.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.9990 chunk 200 optimal weight: 4.9990 chunk 77 optimal weight: 3.9990 chunk 122 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS B 228 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 321 GLN B 580 ASN C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 321 GLN C 580 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.192477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.138461 restraints weight = 17633.806| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.03 r_work: 0.3563 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3462 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.0877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 16557 Z= 0.205 Angle : 0.594 9.333 22497 Z= 0.317 Chirality : 0.045 0.307 2469 Planarity : 0.005 0.044 2913 Dihedral : 6.542 51.763 2440 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 4.90 % Allowed : 20.00 % Favored : 75.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.18), residues: 1989 helix: 2.55 (0.20), residues: 648 sheet: 0.74 (0.23), residues: 504 loop : -0.88 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 264 TYR 0.017 0.002 TYR C 301 PHE 0.019 0.002 PHE A 287 TRP 0.009 0.002 TRP C 539 HIS 0.006 0.001 HIS B 657 Details of bonding type rmsd covalent geometry : bond 0.00482 (16536) covalent geometry : angle 0.58760 (22449) SS BOND : bond 0.00550 ( 15) SS BOND : angle 1.83347 ( 30) hydrogen bonds : bond 0.05651 ( 789) hydrogen bonds : angle 4.98739 ( 2328) link_NAG-ASN : bond 0.00416 ( 6) link_NAG-ASN : angle 2.22286 ( 18) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 197 time to evaluate : 0.618 Fit side-chains REVERT: A 235 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7671 (mmpt) REVERT: A 400 THR cc_start: 0.7498 (p) cc_final: 0.7236 (t) REVERT: A 762 SER cc_start: 0.7836 (t) cc_final: 0.7406 (p) REVERT: B 144 GLU cc_start: 0.7754 (pt0) cc_final: 0.7482 (pt0) REVERT: B 349 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7695 (ttpt) REVERT: B 505 ARG cc_start: 0.5715 (OUTLIER) cc_final: 0.4344 (pmm-80) REVERT: C 144 GLU cc_start: 0.7800 (pt0) cc_final: 0.6250 (tp30) REVERT: C 297 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8582 (ttp) REVERT: C 320 LYS cc_start: 0.8552 (tttp) cc_final: 0.8103 (ttmm) REVERT: C 349 LYS cc_start: 0.8173 (OUTLIER) cc_final: 0.7729 (ttpt) REVERT: C 530 GLU cc_start: 0.7787 (pt0) cc_final: 0.7468 (mt-10) REVERT: C 544 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7664 (mtpt) REVERT: C 768 SER cc_start: 0.8016 (t) cc_final: 0.7373 (m) outliers start: 83 outliers final: 33 residues processed: 256 average time/residue: 0.5350 time to fit residues: 153.5634 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 186 time to evaluate : 0.711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 544 LYS Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 146 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 160 optimal weight: 0.6980 chunk 22 optimal weight: 3.9990 chunk 172 optimal weight: 3.9990 chunk 56 optimal weight: 0.2980 chunk 164 optimal weight: 3.9990 chunk 127 optimal weight: 9.9990 chunk 1 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 155 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 228 HIS B 172 GLN B 228 HIS ** B 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.190682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.136952 restraints weight = 17740.523| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.16 r_work: 0.3530 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3425 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 16557 Z= 0.222 Angle : 0.610 9.305 22497 Z= 0.326 Chirality : 0.046 0.322 2469 Planarity : 0.005 0.042 2913 Dihedral : 6.316 56.101 2411 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 5.66 % Allowed : 20.47 % Favored : 73.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.18), residues: 1989 helix: 2.44 (0.20), residues: 648 sheet: 0.65 (0.23), residues: 504 loop : -0.99 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 264 TYR 0.016 0.002 TYR B 301 PHE 0.020 0.002 PHE A 287 TRP 0.009 0.002 TRP B 354 HIS 0.006 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00527 (16536) covalent geometry : angle 0.60337 (22449) SS BOND : bond 0.00612 ( 15) SS BOND : angle 1.85104 ( 30) hydrogen bonds : bond 0.05742 ( 789) hydrogen bonds : angle 4.86902 ( 2328) link_NAG-ASN : bond 0.00443 ( 6) link_NAG-ASN : angle 2.37844 ( 18) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 187 time to evaluate : 0.542 Fit side-chains REVERT: A 235 LYS cc_start: 0.8107 (OUTLIER) cc_final: 0.7673 (mmpt) REVERT: A 391 ILE cc_start: 0.6945 (OUTLIER) cc_final: 0.6524 (pt) REVERT: A 400 THR cc_start: 0.7505 (p) cc_final: 0.7243 (t) REVERT: A 762 SER cc_start: 0.7791 (t) cc_final: 0.7178 (p) REVERT: B 144 GLU cc_start: 0.7722 (pt0) cc_final: 0.7442 (pt0) REVERT: B 310 GLU cc_start: 0.7493 (mp0) cc_final: 0.7263 (mp0) REVERT: B 349 LYS cc_start: 0.8125 (OUTLIER) cc_final: 0.7652 (ttpt) REVERT: C 128 GLU cc_start: 0.7475 (OUTLIER) cc_final: 0.7176 (mt-10) REVERT: C 144 GLU cc_start: 0.7784 (pt0) cc_final: 0.7273 (pt0) REVERT: C 297 MET cc_start: 0.8850 (OUTLIER) cc_final: 0.8646 (ttp) REVERT: C 320 LYS cc_start: 0.8561 (tttp) cc_final: 0.8063 (ttmm) REVERT: C 349 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7684 (ttpt) REVERT: C 374 GLU cc_start: 0.8204 (mt-10) cc_final: 0.7702 (tt0) REVERT: C 391 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6758 (pt) REVERT: C 642 THR cc_start: 0.9182 (OUTLIER) cc_final: 0.8943 (t) REVERT: C 661 ARG cc_start: 0.8388 (OUTLIER) cc_final: 0.7748 (ttt180) REVERT: C 731 MET cc_start: 0.7972 (ttp) cc_final: 0.7725 (tmm) REVERT: C 768 SER cc_start: 0.7934 (t) cc_final: 0.7278 (m) outliers start: 96 outliers final: 38 residues processed: 257 average time/residue: 0.5269 time to fit residues: 151.6414 Evaluate side-chains 225 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 178 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 233 GLU Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 347 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 456 LEU Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 297 MET Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 175 optimal weight: 0.8980 chunk 13 optimal weight: 0.0970 chunk 187 optimal weight: 0.6980 chunk 161 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 151 optimal weight: 1.9990 chunk 156 optimal weight: 6.9990 chunk 91 optimal weight: 0.0870 chunk 36 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 113 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 HIS A 228 HIS A 514 GLN B 94 HIS B 172 GLN C 94 HIS C 172 GLN C 514 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.190808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.132917 restraints weight = 17611.879| |-----------------------------------------------------------------------------| r_work (start): 0.3617 rms_B_bonded: 1.89 r_work: 0.3533 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3429 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16557 Z= 0.104 Angle : 0.473 8.508 22497 Z= 0.252 Chirality : 0.040 0.282 2469 Planarity : 0.003 0.043 2913 Dihedral : 5.640 54.074 2408 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.89 % Allowed : 22.54 % Favored : 73.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.19), residues: 1989 helix: 2.65 (0.20), residues: 648 sheet: 0.72 (0.23), residues: 495 loop : -0.70 (0.20), residues: 846 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 178 TYR 0.012 0.001 TYR A 653 PHE 0.012 0.001 PHE A 384 TRP 0.007 0.001 TRP A 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00222 (16536) covalent geometry : angle 0.46732 (22449) SS BOND : bond 0.00300 ( 15) SS BOND : angle 1.40202 ( 30) hydrogen bonds : bond 0.04208 ( 789) hydrogen bonds : angle 4.48632 ( 2328) link_NAG-ASN : bond 0.00458 ( 6) link_NAG-ASN : angle 2.11614 ( 18) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 196 time to evaluate : 0.607 Fit side-chains REVERT: A 167 ASP cc_start: 0.7733 (p0) cc_final: 0.7502 (p0) REVERT: A 391 ILE cc_start: 0.6841 (mt) cc_final: 0.6457 (pt) REVERT: A 400 THR cc_start: 0.7443 (p) cc_final: 0.7159 (t) REVERT: A 762 SER cc_start: 0.7748 (t) cc_final: 0.7137 (p) REVERT: B 349 LYS cc_start: 0.8080 (OUTLIER) cc_final: 0.7635 (ttpt) REVERT: B 391 ILE cc_start: 0.7001 (OUTLIER) cc_final: 0.6722 (pt) REVERT: B 507 GLN cc_start: 0.4669 (OUTLIER) cc_final: 0.4444 (tm-30) REVERT: B 530 GLU cc_start: 0.7856 (pt0) cc_final: 0.7492 (mt-10) REVERT: C 129 GLN cc_start: 0.7880 (OUTLIER) cc_final: 0.7646 (mt0) REVERT: C 320 LYS cc_start: 0.8489 (tttp) cc_final: 0.8032 (ttmm) REVERT: C 349 LYS cc_start: 0.8116 (OUTLIER) cc_final: 0.7639 (ttpt) REVERT: C 374 GLU cc_start: 0.8151 (mt-10) cc_final: 0.7662 (tt0) REVERT: C 391 ILE cc_start: 0.6923 (OUTLIER) cc_final: 0.6622 (pt) REVERT: C 436 VAL cc_start: 0.7338 (OUTLIER) cc_final: 0.7088 (m) REVERT: C 530 GLU cc_start: 0.7694 (pt0) cc_final: 0.7370 (mt-10) REVERT: C 768 SER cc_start: 0.7859 (t) cc_final: 0.7264 (m) outliers start: 66 outliers final: 29 residues processed: 239 average time/residue: 0.4968 time to fit residues: 134.1905 Evaluate side-chains 228 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 192 time to evaluate : 0.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 391 ILE Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 95 optimal weight: 5.9990 chunk 23 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 130 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 66 optimal weight: 7.9990 chunk 63 optimal weight: 0.0980 chunk 106 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 136 optimal weight: 0.2980 chunk 114 optimal weight: 2.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 228 HIS B 172 GLN B 202 ASN B 228 HIS C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.188217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.129707 restraints weight = 17564.732| |-----------------------------------------------------------------------------| r_work (start): 0.3573 rms_B_bonded: 1.88 r_work: 0.3484 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3377 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 16557 Z= 0.172 Angle : 0.549 8.556 22497 Z= 0.291 Chirality : 0.043 0.294 2469 Planarity : 0.004 0.043 2913 Dihedral : 5.576 51.656 2404 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 5.01 % Allowed : 21.47 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.06 (0.19), residues: 1989 helix: 2.61 (0.20), residues: 648 sheet: 0.78 (0.23), residues: 504 loop : -0.93 (0.19), residues: 837 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 342 TYR 0.022 0.001 TYR C 301 PHE 0.016 0.002 PHE A 287 TRP 0.008 0.001 TRP C 539 HIS 0.005 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00407 (16536) covalent geometry : angle 0.54103 (22449) SS BOND : bond 0.00584 ( 15) SS BOND : angle 1.96868 ( 30) hydrogen bonds : bond 0.04988 ( 789) hydrogen bonds : angle 4.59903 ( 2328) link_NAG-ASN : bond 0.00360 ( 6) link_NAG-ASN : angle 2.12143 ( 18) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 191 time to evaluate : 0.655 Fit side-chains REVERT: A 235 LYS cc_start: 0.8132 (OUTLIER) cc_final: 0.7692 (mmpt) REVERT: A 391 ILE cc_start: 0.6908 (OUTLIER) cc_final: 0.6496 (pt) REVERT: A 400 THR cc_start: 0.7475 (p) cc_final: 0.7199 (t) REVERT: A 762 SER cc_start: 0.7790 (t) cc_final: 0.7185 (p) REVERT: B 310 GLU cc_start: 0.7425 (mp0) cc_final: 0.7191 (mp0) REVERT: B 349 LYS cc_start: 0.8106 (OUTLIER) cc_final: 0.7665 (ttpt) REVERT: B 460 LEU cc_start: 0.5958 (OUTLIER) cc_final: 0.5698 (tt) REVERT: B 507 GLN cc_start: 0.4584 (OUTLIER) cc_final: 0.4334 (tm-30) REVERT: C 128 GLU cc_start: 0.7422 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: C 320 LYS cc_start: 0.8526 (tttp) cc_final: 0.8069 (ttmm) REVERT: C 349 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7680 (ttpt) REVERT: C 374 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7790 (tt0) REVERT: C 391 ILE cc_start: 0.6964 (OUTLIER) cc_final: 0.6654 (pt) REVERT: C 530 GLU cc_start: 0.7723 (pt0) cc_final: 0.7425 (mt-10) REVERT: C 661 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7710 (ttt180) REVERT: C 768 SER cc_start: 0.7908 (t) cc_final: 0.7312 (m) outliers start: 85 outliers final: 43 residues processed: 251 average time/residue: 0.4964 time to fit residues: 140.6334 Evaluate side-chains 238 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 186 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain B residue 721 THR Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 250 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 661 ARG Chi-restraints excluded: chain C residue 721 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 156 optimal weight: 7.9990 chunk 118 optimal weight: 0.9980 chunk 145 optimal weight: 6.9990 chunk 80 optimal weight: 0.9990 chunk 182 optimal weight: 0.0870 chunk 126 optimal weight: 9.9990 chunk 79 optimal weight: 3.9990 chunk 164 optimal weight: 0.4980 chunk 69 optimal weight: 0.0040 chunk 55 optimal weight: 0.9980 chunk 180 optimal weight: 0.5980 overall best weight: 0.4370 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN A 228 HIS A 580 ASN B 172 GLN B 228 HIS C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.191200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.134041 restraints weight = 17582.097| |-----------------------------------------------------------------------------| r_work (start): 0.3624 rms_B_bonded: 1.99 r_work: 0.3533 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 16557 Z= 0.099 Angle : 0.466 8.756 22497 Z= 0.247 Chirality : 0.039 0.270 2469 Planarity : 0.003 0.043 2913 Dihedral : 5.232 52.787 2404 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 4.31 % Allowed : 22.65 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.19), residues: 1989 helix: 2.73 (0.20), residues: 648 sheet: 0.80 (0.23), residues: 516 loop : -0.76 (0.20), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.022 0.001 TYR A 301 PHE 0.015 0.001 PHE A 795 TRP 0.006 0.001 TRP B 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00209 (16536) covalent geometry : angle 0.46111 (22449) SS BOND : bond 0.00295 ( 15) SS BOND : angle 1.15899 ( 30) hydrogen bonds : bond 0.03955 ( 789) hydrogen bonds : angle 4.34186 ( 2328) link_NAG-ASN : bond 0.00431 ( 6) link_NAG-ASN : angle 2.00667 ( 18) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 195 time to evaluate : 0.447 Fit side-chains REVERT: A 235 LYS cc_start: 0.8083 (OUTLIER) cc_final: 0.7633 (mmpt) REVERT: A 391 ILE cc_start: 0.6850 (mt) cc_final: 0.6466 (pt) REVERT: A 400 THR cc_start: 0.7425 (p) cc_final: 0.7135 (t) REVERT: A 762 SER cc_start: 0.7709 (t) cc_final: 0.7089 (p) REVERT: B 349 LYS cc_start: 0.8026 (OUTLIER) cc_final: 0.7526 (ttpt) REVERT: B 507 GLN cc_start: 0.4617 (OUTLIER) cc_final: 0.4372 (tm-30) REVERT: B 530 GLU cc_start: 0.7747 (pt0) cc_final: 0.7414 (mt-10) REVERT: C 129 GLN cc_start: 0.7822 (OUTLIER) cc_final: 0.7584 (mt0) REVERT: C 320 LYS cc_start: 0.8464 (tttp) cc_final: 0.7979 (ttmm) REVERT: C 349 LYS cc_start: 0.8079 (OUTLIER) cc_final: 0.7586 (ttpt) REVERT: C 374 GLU cc_start: 0.8084 (mt-10) cc_final: 0.7637 (tt0) REVERT: C 391 ILE cc_start: 0.6913 (mt) cc_final: 0.6628 (pt) REVERT: C 436 VAL cc_start: 0.7330 (OUTLIER) cc_final: 0.7116 (m) REVERT: C 530 GLU cc_start: 0.7608 (pt0) cc_final: 0.7310 (mt-10) REVERT: C 642 THR cc_start: 0.8988 (OUTLIER) cc_final: 0.8703 (m) REVERT: C 704 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8123 (mm-30) REVERT: C 731 MET cc_start: 0.7893 (ttp) cc_final: 0.7609 (tmm) outliers start: 73 outliers final: 37 residues processed: 243 average time/residue: 0.4929 time to fit residues: 135.2315 Evaluate side-chains 231 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 187 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 194 optimal weight: 10.0000 chunk 168 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 0.9980 chunk 160 optimal weight: 2.9990 chunk 127 optimal weight: 10.0000 chunk 134 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 150 optimal weight: 5.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 228 HIS ** B 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 512 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4185 r_free = 0.4185 target = 0.189858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.136517 restraints weight = 17472.733| |-----------------------------------------------------------------------------| r_work (start): 0.3660 rms_B_bonded: 2.00 r_work: 0.3537 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3435 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 16557 Z= 0.257 Angle : 0.631 8.654 22497 Z= 0.335 Chirality : 0.047 0.299 2469 Planarity : 0.005 0.044 2913 Dihedral : 5.687 50.257 2400 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 5.07 % Allowed : 21.95 % Favored : 72.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.16 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.19), residues: 1989 helix: 2.35 (0.20), residues: 666 sheet: 0.65 (0.23), residues: 498 loop : -0.96 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 342 TYR 0.020 0.002 TYR C 301 PHE 0.019 0.002 PHE A 287 TRP 0.011 0.002 TRP C 539 HIS 0.007 0.001 HIS A 657 Details of bonding type rmsd covalent geometry : bond 0.00619 (16536) covalent geometry : angle 0.62388 (22449) SS BOND : bond 0.00651 ( 15) SS BOND : angle 2.02678 ( 30) hydrogen bonds : bond 0.05775 ( 789) hydrogen bonds : angle 4.71682 ( 2328) link_NAG-ASN : bond 0.00325 ( 6) link_NAG-ASN : angle 2.23590 ( 18) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 184 time to evaluate : 0.601 Fit side-chains REVERT: A 144 GLU cc_start: 0.7584 (pt0) cc_final: 0.5983 (tp30) REVERT: A 235 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7694 (mmpt) REVERT: A 391 ILE cc_start: 0.6932 (OUTLIER) cc_final: 0.6539 (pt) REVERT: A 400 THR cc_start: 0.7537 (p) cc_final: 0.7270 (t) REVERT: A 762 SER cc_start: 0.7781 (t) cc_final: 0.7182 (p) REVERT: B 349 LYS cc_start: 0.8126 (OUTLIER) cc_final: 0.7615 (ttpt) REVERT: B 507 GLN cc_start: 0.4558 (OUTLIER) cc_final: 0.4309 (tm-30) REVERT: C 128 GLU cc_start: 0.7461 (OUTLIER) cc_final: 0.6947 (mm-30) REVERT: C 136 ARG cc_start: 0.4127 (OUTLIER) cc_final: 0.3484 (ttp-170) REVERT: C 320 LYS cc_start: 0.8508 (tttp) cc_final: 0.8046 (ttmm) REVERT: C 349 LYS cc_start: 0.8194 (OUTLIER) cc_final: 0.7708 (ttpt) REVERT: C 374 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7789 (tt0) REVERT: C 391 ILE cc_start: 0.6989 (OUTLIER) cc_final: 0.6667 (pt) REVERT: C 530 GLU cc_start: 0.7769 (pt0) cc_final: 0.7459 (mt-10) REVERT: C 661 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7730 (ttt180) REVERT: C 768 SER cc_start: 0.7974 (t) cc_final: 0.7330 (m) outliers start: 86 outliers final: 45 residues processed: 251 average time/residue: 0.5168 time to fit residues: 145.8356 Evaluate side-chains 230 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 176 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 313 SER Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 143 THR Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 128 GLU Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 136 ARG Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Chi-restraints excluded: chain C residue 661 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 132 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 74 optimal weight: 0.8980 chunk 162 optimal weight: 5.9990 chunk 122 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 175 optimal weight: 0.9980 chunk 185 optimal weight: 0.9990 chunk 47 optimal weight: 1.9990 chunk 92 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 228 HIS B 172 GLN B 228 HIS C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4170 r_free = 0.4170 target = 0.189137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.131265 restraints weight = 17453.834| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 1.86 r_work: 0.3502 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3398 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 16557 Z= 0.128 Angle : 0.512 9.129 22497 Z= 0.270 Chirality : 0.041 0.280 2469 Planarity : 0.004 0.045 2913 Dihedral : 5.342 52.098 2400 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.95 % Allowed : 23.24 % Favored : 72.80 % 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 are not related in a simple way. whole: 1.07 (0.19), residues: 1989 helix: 2.59 (0.20), residues: 648 sheet: 0.71 (0.23), residues: 516 loop : -0.86 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 385 TYR 0.021 0.001 TYR A 301 PHE 0.019 0.001 PHE A 795 TRP 0.007 0.001 TRP B 354 HIS 0.004 0.001 HIS A 534 Details of bonding type rmsd covalent geometry : bond 0.00288 (16536) covalent geometry : angle 0.50660 (22449) SS BOND : bond 0.00373 ( 15) SS BOND : angle 1.26899 ( 30) hydrogen bonds : bond 0.04476 ( 789) hydrogen bonds : angle 4.46947 ( 2328) link_NAG-ASN : bond 0.00390 ( 6) link_NAG-ASN : angle 2.10391 ( 18) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 188 time to evaluate : 0.642 Fit side-chains REVERT: A 144 GLU cc_start: 0.7565 (pt0) cc_final: 0.7296 (pt0) REVERT: A 235 LYS cc_start: 0.8123 (OUTLIER) cc_final: 0.7676 (mmpt) REVERT: A 391 ILE cc_start: 0.6917 (OUTLIER) cc_final: 0.6551 (pt) REVERT: A 400 THR cc_start: 0.7475 (p) cc_final: 0.7201 (t) REVERT: A 557 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8161 (ttm-80) REVERT: A 762 SER cc_start: 0.7759 (t) cc_final: 0.7155 (p) REVERT: B 172 GLN cc_start: 0.7043 (OUTLIER) cc_final: 0.6733 (pm20) REVERT: B 349 LYS cc_start: 0.8081 (OUTLIER) cc_final: 0.7630 (ttpt) REVERT: B 507 GLN cc_start: 0.4595 (OUTLIER) cc_final: 0.4374 (tm-30) REVERT: C 320 LYS cc_start: 0.8462 (tttp) cc_final: 0.8010 (ttmm) REVERT: C 349 LYS cc_start: 0.8139 (OUTLIER) cc_final: 0.7644 (ttpt) REVERT: C 374 GLU cc_start: 0.8125 (mt-10) cc_final: 0.7741 (tt0) REVERT: C 391 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6671 (pt) REVERT: C 530 GLU cc_start: 0.7703 (pt0) cc_final: 0.7393 (mt-10) REVERT: C 704 GLU cc_start: 0.8410 (mt-10) cc_final: 0.8171 (mm-30) REVERT: C 731 MET cc_start: 0.7947 (ttp) cc_final: 0.7698 (tmm) REVERT: C 768 SER cc_start: 0.7938 (t) cc_final: 0.7308 (m) outliers start: 67 outliers final: 41 residues processed: 233 average time/residue: 0.5023 time to fit residues: 132.1031 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 185 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 167 optimal weight: 2.9990 chunk 138 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 6.9990 chunk 112 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 105 optimal weight: 6.9990 chunk 152 optimal weight: 0.7980 chunk 93 optimal weight: 0.4980 chunk 43 optimal weight: 0.9980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS B 228 HIS C 172 GLN ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.188752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.130677 restraints weight = 17478.151| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 1.87 r_work: 0.3499 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3394 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3394 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 16557 Z= 0.140 Angle : 0.532 9.470 22497 Z= 0.279 Chirality : 0.041 0.277 2469 Planarity : 0.004 0.045 2913 Dihedral : 5.315 51.477 2400 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.60 % Allowed : 23.66 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.19), residues: 1989 helix: 2.62 (0.20), residues: 648 sheet: 0.70 (0.23), residues: 516 loop : -0.86 (0.19), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 385 TYR 0.023 0.001 TYR C 301 PHE 0.024 0.001 PHE B 795 TRP 0.007 0.001 TRP B 354 HIS 0.011 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00322 (16536) covalent geometry : angle 0.52744 (22449) SS BOND : bond 0.00419 ( 15) SS BOND : angle 1.39279 ( 30) hydrogen bonds : bond 0.04593 ( 789) hydrogen bonds : angle 4.45723 ( 2328) link_NAG-ASN : bond 0.00369 ( 6) link_NAG-ASN : angle 2.04213 ( 18) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 185 time to evaluate : 0.518 Fit side-chains REVERT: A 144 GLU cc_start: 0.7590 (pt0) cc_final: 0.7342 (pt0) REVERT: A 235 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7679 (mmpt) REVERT: A 391 ILE cc_start: 0.6936 (OUTLIER) cc_final: 0.6551 (pt) REVERT: A 400 THR cc_start: 0.7489 (p) cc_final: 0.7213 (t) REVERT: A 557 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8177 (ttm-80) REVERT: A 762 SER cc_start: 0.7770 (t) cc_final: 0.7172 (p) REVERT: B 349 LYS cc_start: 0.8074 (OUTLIER) cc_final: 0.7625 (ttpt) REVERT: B 385 ARG cc_start: 0.7784 (tmt170) cc_final: 0.7559 (tmt170) REVERT: B 507 GLN cc_start: 0.4601 (OUTLIER) cc_final: 0.4379 (tm-30) REVERT: B 530 GLU cc_start: 0.7894 (pt0) cc_final: 0.7532 (mt-10) REVERT: C 320 LYS cc_start: 0.8477 (tttp) cc_final: 0.8031 (ttmm) REVERT: C 349 LYS cc_start: 0.8155 (OUTLIER) cc_final: 0.7666 (ttpt) REVERT: C 374 GLU cc_start: 0.8136 (mt-10) cc_final: 0.7766 (tt0) REVERT: C 391 ILE cc_start: 0.6938 (OUTLIER) cc_final: 0.6669 (pt) REVERT: C 520 MET cc_start: 0.7211 (ttm) cc_final: 0.6911 (ttm) REVERT: C 530 GLU cc_start: 0.7720 (pt0) cc_final: 0.7417 (mt-10) REVERT: C 704 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8191 (mm-30) REVERT: C 731 MET cc_start: 0.7960 (ttp) cc_final: 0.7654 (tmm) REVERT: C 768 SER cc_start: 0.7933 (t) cc_final: 0.7298 (m) outliers start: 61 outliers final: 44 residues processed: 227 average time/residue: 0.4795 time to fit residues: 123.7237 Evaluate side-chains 234 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 183 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 93 optimal weight: 0.2980 chunk 20 optimal weight: 0.9990 chunk 148 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 89 optimal weight: 5.9990 chunk 198 optimal weight: 6.9990 chunk 18 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 56 optimal weight: 0.4980 chunk 7 optimal weight: 2.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 228 HIS ** A 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 172 GLN B 228 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.187304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.129020 restraints weight = 17448.237| |-----------------------------------------------------------------------------| r_work (start): 0.3560 rms_B_bonded: 1.86 r_work: 0.3470 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3364 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16557 Z= 0.184 Angle : 0.581 9.224 22497 Z= 0.306 Chirality : 0.043 0.286 2469 Planarity : 0.004 0.044 2913 Dihedral : 5.500 50.398 2400 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 4.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 3.54 % Allowed : 23.60 % Favored : 72.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1989 helix: 2.54 (0.20), residues: 648 sheet: 0.54 (0.23), residues: 510 loop : -0.87 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 385 TYR 0.022 0.002 TYR A 301 PHE 0.024 0.002 PHE B 795 TRP 0.010 0.001 TRP C 539 HIS 0.011 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00435 (16536) covalent geometry : angle 0.57527 (22449) SS BOND : bond 0.00523 ( 15) SS BOND : angle 1.63396 ( 30) hydrogen bonds : bond 0.05144 ( 789) hydrogen bonds : angle 4.59804 ( 2328) link_NAG-ASN : bond 0.00324 ( 6) link_NAG-ASN : angle 2.13261 ( 18) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3978 Ramachandran restraints generated. 1989 Oldfield, 0 Emsley, 1989 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 182 time to evaluate : 0.638 Fit side-chains REVERT: A 144 GLU cc_start: 0.7595 (pt0) cc_final: 0.7327 (pt0) REVERT: A 235 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7694 (mmpt) REVERT: A 391 ILE cc_start: 0.6930 (OUTLIER) cc_final: 0.6559 (pt) REVERT: A 400 THR cc_start: 0.7495 (p) cc_final: 0.7237 (t) REVERT: A 557 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8196 (ttm-80) REVERT: A 762 SER cc_start: 0.7751 (t) cc_final: 0.7164 (p) REVERT: B 172 GLN cc_start: 0.7006 (OUTLIER) cc_final: 0.6750 (pm20) REVERT: B 349 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7678 (ttpt) REVERT: B 507 GLN cc_start: 0.4714 (OUTLIER) cc_final: 0.4478 (tm-30) REVERT: C 320 LYS cc_start: 0.8505 (tttp) cc_final: 0.8044 (ttmm) REVERT: C 349 LYS cc_start: 0.8181 (OUTLIER) cc_final: 0.7684 (ttpt) REVERT: C 374 GLU cc_start: 0.8115 (mt-10) cc_final: 0.7784 (tt0) REVERT: C 391 ILE cc_start: 0.6988 (OUTLIER) cc_final: 0.6673 (pt) REVERT: C 520 MET cc_start: 0.7294 (ttm) cc_final: 0.6988 (ttm) REVERT: C 530 GLU cc_start: 0.7765 (pt0) cc_final: 0.7447 (mt-10) REVERT: C 704 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8263 (mm-30) REVERT: C 731 MET cc_start: 0.7993 (ttp) cc_final: 0.7648 (tmm) REVERT: C 768 SER cc_start: 0.7960 (t) cc_final: 0.7307 (m) outliers start: 60 outliers final: 47 residues processed: 229 average time/residue: 0.4714 time to fit residues: 122.6602 Evaluate side-chains 236 residues out of total 1695 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 181 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 ILE Chi-restraints excluded: chain A residue 207 CYS Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 230 THR Chi-restraints excluded: chain A residue 235 LYS Chi-restraints excluded: chain A residue 250 THR Chi-restraints excluded: chain A residue 267 THR Chi-restraints excluded: chain A residue 268 THR Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain A residue 378 SER Chi-restraints excluded: chain A residue 391 ILE Chi-restraints excluded: chain A residue 397 THR Chi-restraints excluded: chain A residue 436 VAL Chi-restraints excluded: chain A residue 524 VAL Chi-restraints excluded: chain A residue 557 ARG Chi-restraints excluded: chain A residue 579 ASP Chi-restraints excluded: chain A residue 590 SER Chi-restraints excluded: chain A residue 591 SER Chi-restraints excluded: chain A residue 620 ASN Chi-restraints excluded: chain A residue 721 THR Chi-restraints excluded: chain B residue 104 ILE Chi-restraints excluded: chain B residue 172 GLN Chi-restraints excluded: chain B residue 207 CYS Chi-restraints excluded: chain B residue 220 THR Chi-restraints excluded: chain B residue 230 THR Chi-restraints excluded: chain B residue 250 THR Chi-restraints excluded: chain B residue 268 THR Chi-restraints excluded: chain B residue 341 THR Chi-restraints excluded: chain B residue 349 LYS Chi-restraints excluded: chain B residue 352 VAL Chi-restraints excluded: chain B residue 378 SER Chi-restraints excluded: chain B residue 397 THR Chi-restraints excluded: chain B residue 421 MET Chi-restraints excluded: chain B residue 505 ARG Chi-restraints excluded: chain B residue 507 GLN Chi-restraints excluded: chain B residue 590 SER Chi-restraints excluded: chain B residue 667 VAL Chi-restraints excluded: chain C residue 104 ILE Chi-restraints excluded: chain C residue 129 GLN Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 185 ILE Chi-restraints excluded: chain C residue 207 CYS Chi-restraints excluded: chain C residue 220 THR Chi-restraints excluded: chain C residue 268 THR Chi-restraints excluded: chain C residue 341 THR Chi-restraints excluded: chain C residue 349 LYS Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 391 ILE Chi-restraints excluded: chain C residue 397 THR Chi-restraints excluded: chain C residue 436 VAL Chi-restraints excluded: chain C residue 506 LEU Chi-restraints excluded: chain C residue 579 ASP Chi-restraints excluded: chain C residue 591 SER Chi-restraints excluded: chain C residue 642 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 201 random chunks: chunk 154 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 45 optimal weight: 0.9980 chunk 139 optimal weight: 3.9990 chunk 85 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 chunk 190 optimal weight: 0.9980 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 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 228 HIS ** C 263 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 512 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.187538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.129220 restraints weight = 17415.104| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.86 r_work: 0.3482 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3376 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.111 16557 Z= 0.173 Angle : 0.774 59.176 22497 Z= 0.440 Chirality : 0.043 0.403 2469 Planarity : 0.004 0.045 2913 Dihedral : 5.524 50.412 2400 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 3.66 % Allowed : 23.60 % Favored : 72.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.19), residues: 1989 helix: 2.54 (0.20), residues: 648 sheet: 0.55 (0.23), residues: 510 loop : -0.86 (0.19), residues: 831 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 385 TYR 0.012 0.001 TYR C 301 PHE 0.023 0.002 PHE B 795 TRP 0.009 0.001 TRP C 539 HIS 0.010 0.001 HIS C 512 Details of bonding type rmsd covalent geometry : bond 0.00405 (16536) covalent geometry : angle 0.77060 (22449) SS BOND : bond 0.00475 ( 15) SS BOND : angle 1.57690 ( 30) hydrogen bonds : bond 0.05066 ( 789) hydrogen bonds : angle 4.59824 ( 2328) link_NAG-ASN : bond 0.00310 ( 6) link_NAG-ASN : angle 2.13020 ( 18) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7050.45 seconds wall clock time: 120 minutes 22.43 seconds (7222.43 seconds total)