Starting phenix.real_space_refine on Fri Jul 3 02:27:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.map" model { file = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kna_22937/07_2026/7kna_22937.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 48 5.16 5 C 7314 2.51 5 N 1990 2.21 5 O 2241 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11593 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 3755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3755 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 79 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 58 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "B" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3751 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "C" Number of atoms: 3751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3751 Classifications: {'peptide': 483} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 19, 'TRANS': 463} Chain breaks: 1 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 104 Unresolved non-hydrogen dihedrals: 62 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 7, 'ASN:plan1': 4, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "B" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Chain: "C" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.53, per 1000 atoms: 0.22 Number of scatterers: 11593 At special positions: 0 Unit cell: (92.4, 85.05, 144.9, 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 48 16.00 O 2241 8.00 N 1990 7.00 C 7314 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 14 " - pdb=" SG CYS A 630 " distance=2.03 Simple disulfide: pdb=" SG CYS A 52 " - pdb=" SG CYS A 283 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 77 " distance=2.03 Simple disulfide: pdb=" SG CYS A 100 " - pdb=" SG CYS A 145 " distance=2.02 Simple disulfide: pdb=" SG CYS A 287 " - pdb=" SG CYS A 311 " distance=2.02 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS A 641 " distance=2.06 Simple disulfide: pdb=" SG CYS B 14 " - pdb=" SG CYS B 630 " distance=2.03 Simple disulfide: pdb=" SG CYS B 52 " - pdb=" SG CYS B 283 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 77 " distance=2.03 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 145 " distance=2.02 Simple disulfide: pdb=" SG CYS B 287 " - pdb=" SG CYS B 311 " distance=2.02 Simple disulfide: pdb=" SG CYS B 637 " - pdb=" SG CYS B 641 " distance=2.06 Simple disulfide: pdb=" SG CYS C 14 " - pdb=" SG CYS C 630 " distance=2.03 Simple disulfide: pdb=" SG CYS C 52 " - pdb=" SG CYS C 283 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 77 " distance=2.03 Simple disulfide: pdb=" SG CYS C 100 " - pdb=" SG CYS C 145 " distance=2.02 Simple disulfide: pdb=" SG CYS C 287 " - pdb=" SG CYS C 311 " distance=2.02 Simple disulfide: pdb=" SG CYS C 637 " - pdb=" SG CYS C 641 " distance=2.06 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 BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " NAG-ASN " NAG A 901 " - " ASN A 21 " " NAG A 902 " - " ASN A 33 " " NAG A 903 " - " ASN A 295 " " NAG A 904 " - " ASN A 647 " " NAG B 901 " - " ASN B 21 " " NAG B 902 " - " ASN B 33 " " NAG B 903 " - " ASN B 295 " " NAG B 904 " - " ASN B 647 " " NAG C 901 " - " ASN C 21 " " NAG C 902 " - " ASN C 33 " " NAG C 903 " - " ASN C 295 " " NAG C 904 " - " ASN C 647 " " NAG D 1 " - " ASN A 97 " " NAG E 1 " - " ASN A 284 " " NAG F 1 " - " ASN B 97 " " NAG G 1 " - " ASN B 284 " " NAG H 1 " - " ASN C 97 " " NAG I 1 " - " ASN C 284 " Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 515.4 milliseconds 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2694 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 33 sheets defined 26.7% alpha, 25.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU A 78 " --> pdb=" O PRO A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 115 Processing helix chain 'A' and resid 193 through 202 Processing helix chain 'A' and resid 530 through 551 Processing helix chain 'A' and resid 567 through 620 removed outlier: 3.649A pdb=" N GLU A 598 " --> pdb=" O LEU A 594 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ARG A 599 " --> pdb=" O LEU A 595 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 618 " --> pdb=" O LYS A 614 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 647 removed outlier: 3.523A pdb=" N SER A 644 " --> pdb=" O THR A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 652 through 654 No H-bonds generated for 'chain 'A' and resid 652 through 654' Processing helix chain 'A' and resid 655 through 662 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU B 78 " --> pdb=" O PRO B 75 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 115 Processing helix chain 'B' and resid 193 through 202 Processing helix chain 'B' and resid 530 through 551 Processing helix chain 'B' and resid 567 through 620 removed outlier: 3.649A pdb=" N GLU B 598 " --> pdb=" O LEU B 594 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG B 599 " --> pdb=" O LEU B 595 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN B 618 " --> pdb=" O LYS B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 638 through 647 removed outlier: 3.522A pdb=" N SER B 644 " --> pdb=" O THR B 640 " (cutoff:3.500A) Processing helix chain 'B' and resid 652 through 654 No H-bonds generated for 'chain 'B' and resid 652 through 654' Processing helix chain 'B' and resid 655 through 662 Processing helix chain 'C' and resid 66 through 73 Processing helix chain 'C' and resid 74 through 78 removed outlier: 3.772A pdb=" N GLU C 78 " --> pdb=" O PRO C 75 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 115 Processing helix chain 'C' and resid 193 through 202 Processing helix chain 'C' and resid 530 through 551 Processing helix chain 'C' and resid 567 through 620 removed outlier: 3.648A pdb=" N GLU C 598 " --> pdb=" O LEU C 594 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ARG C 599 " --> pdb=" O LEU C 595 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN C 618 " --> pdb=" O LYS C 614 " (cutoff:3.500A) Processing helix chain 'C' and resid 638 through 647 removed outlier: 3.522A pdb=" N SER C 644 " --> pdb=" O THR C 640 " (cutoff:3.500A) Processing helix chain 'C' and resid 652 through 654 No H-bonds generated for 'chain 'C' and resid 652 through 654' Processing helix chain 'C' and resid 655 through 662 Processing sheet with id=AA1, first strand: chain 'A' and resid 525 through 529 Processing sheet with id=AA2, first strand: chain 'A' and resid 25 through 26 Processing sheet with id=AA3, first strand: chain 'A' and resid 39 through 41 Processing sheet with id=AA4, first strand: chain 'A' and resid 43 through 44 Processing sheet with id=AA5, first strand: chain 'A' and resid 51 through 54 removed outlier: 5.919A pdb=" N LEU A 51 " --> pdb=" O HIS A 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS A 283 " --> pdb=" O LEU A 51 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 60 through 62 removed outlier: 6.388A pdb=" N LEU A 60 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE A 89 " --> pdb=" O ILE A 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER A 120 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU A 185 " --> pdb=" O PRO A 260 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER A 120 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS A 145 " --> pdb=" O SER A 152 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 170 through 175 Processing sheet with id=AB2, first strand: chain 'A' and resid 287 through 288 Processing sheet with id=AB3, first strand: chain 'B' and resid 525 through 529 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 26 Processing sheet with id=AB5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AB6, first strand: chain 'B' and resid 43 through 44 Processing sheet with id=AB7, first strand: chain 'B' and resid 51 through 54 removed outlier: 5.919A pdb=" N LEU B 51 " --> pdb=" O HIS B 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS B 283 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 60 through 62 removed outlier: 6.387A pdb=" N LEU B 60 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 89 " --> pdb=" O ILE B 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 118 through 124 removed outlier: 3.760A pdb=" N SER B 120 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU B 185 " --> pdb=" O PRO B 260 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 118 through 124 removed outlier: 3.760A pdb=" N SER B 120 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS B 145 " --> pdb=" O SER B 152 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 170 through 175 Processing sheet with id=AC4, first strand: chain 'B' and resid 287 through 288 Processing sheet with id=AC5, first strand: chain 'C' and resid 525 through 529 Processing sheet with id=AC6, first strand: chain 'C' and resid 25 through 26 Processing sheet with id=AC7, first strand: chain 'C' and resid 39 through 41 Processing sheet with id=AC8, first strand: chain 'C' and resid 43 through 44 Processing sheet with id=AC9, first strand: chain 'C' and resid 51 through 54 removed outlier: 5.920A pdb=" N LEU C 51 " --> pdb=" O HIS C 281 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N CYS C 283 " --> pdb=" O LEU C 51 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 60 through 62 removed outlier: 6.387A pdb=" N LEU C 60 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE C 89 " --> pdb=" O ILE C 274 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER C 120 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N LEU C 185 " --> pdb=" O PRO C 260 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 118 through 124 removed outlier: 3.761A pdb=" N SER C 120 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 142 through 147 removed outlier: 4.737A pdb=" N CYS C 145 " --> pdb=" O SER C 152 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 170 through 175 Processing sheet with id=AD6, first strand: chain 'C' and resid 287 through 288 495 hydrogen bonds defined for protein. 1368 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.99 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.31: 2030 1.31 - 1.45: 3500 1.45 - 1.58: 6255 1.58 - 1.72: 15 1.72 - 1.86: 60 Bond restraints: 11860 Sorted by residual: bond pdb=" NE ARG A 663 " pdb=" CZ ARG A 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.54e+01 bond pdb=" NE ARG C 663 " pdb=" CZ ARG C 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.51e+01 bond pdb=" NE ARG B 663 " pdb=" CZ ARG B 663 " ideal model delta sigma weight residual 1.326 1.381 -0.055 1.10e-02 8.26e+03 2.51e+01 bond pdb=" C CYS A 100 " pdb=" O CYS A 100 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.28e-02 6.10e+03 2.43e+01 bond pdb=" C CYS B 100 " pdb=" O CYS B 100 " ideal model delta sigma weight residual 1.236 1.173 0.063 1.28e-02 6.10e+03 2.40e+01 ... (remaining 11855 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.18: 16054 6.18 - 12.37: 45 12.37 - 18.55: 3 18.55 - 24.73: 0 24.73 - 30.92: 3 Bond angle restraints: 16105 Sorted by residual: angle pdb=" C2 NAG C 902 " pdb=" N2 NAG C 902 " pdb=" C7 NAG C 902 " ideal model delta sigma weight residual 124.56 155.48 -30.92 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C2 NAG B 902 " pdb=" N2 NAG B 902 " pdb=" C7 NAG B 902 " ideal model delta sigma weight residual 124.56 155.47 -30.91 3.00e+00 1.11e-01 1.06e+02 angle pdb=" C2 NAG A 902 " pdb=" N2 NAG A 902 " pdb=" C7 NAG A 902 " ideal model delta sigma weight residual 124.56 155.45 -30.89 3.00e+00 1.11e-01 1.06e+02 angle pdb=" CD1 LEU A 170 " pdb=" CG LEU A 170 " pdb=" CD2 LEU A 170 " ideal model delta sigma weight residual 110.80 92.87 17.93 2.20e+00 2.07e-01 6.64e+01 angle pdb=" CD1 LEU B 170 " pdb=" CG LEU B 170 " pdb=" CD2 LEU B 170 " ideal model delta sigma weight residual 110.80 92.88 17.92 2.20e+00 2.07e-01 6.64e+01 ... (remaining 16100 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 6544 16.36 - 32.72: 246 32.72 - 49.07: 48 49.07 - 65.43: 24 65.43 - 81.79: 9 Dihedral angle restraints: 6871 sinusoidal: 2665 harmonic: 4206 Sorted by residual: dihedral pdb=" CB CYS A 65 " pdb=" SG CYS A 65 " pdb=" SG CYS A 77 " pdb=" CB CYS A 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.72 39.72 1 1.00e+01 1.00e-02 2.22e+01 dihedral pdb=" CB CYS B 65 " pdb=" SG CYS B 65 " pdb=" SG CYS B 77 " pdb=" CB CYS B 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.70 39.70 1 1.00e+01 1.00e-02 2.21e+01 dihedral pdb=" CB CYS C 65 " pdb=" SG CYS C 65 " pdb=" SG CYS C 77 " pdb=" CB CYS C 77 " ideal model delta sinusoidal sigma weight residual -86.00 -125.69 39.69 1 1.00e+01 1.00e-02 2.21e+01 ... (remaining 6868 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 1643 0.134 - 0.268: 137 0.268 - 0.403: 50 0.403 - 0.537: 3 0.537 - 0.671: 3 Chirality restraints: 1836 Sorted by residual: chirality pdb=" C1 NAG I 2 " pdb=" O4 NAG I 1 " pdb=" C2 NAG I 2 " pdb=" O5 NAG I 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.45e+01 chirality pdb=" C1 NAG G 2 " pdb=" O4 NAG G 1 " pdb=" C2 NAG G 2 " pdb=" O5 NAG G 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.32e+01 chirality pdb=" C1 NAG E 2 " pdb=" O4 NAG E 1 " pdb=" C2 NAG E 2 " pdb=" O5 NAG E 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.55 0.15 2.00e-02 2.50e+03 5.27e+01 ... (remaining 1833 not shown) Planarity restraints: 2061 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN C 97 " -0.034 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" CG ASN C 97 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN C 97 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN C 97 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG H 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 97 " -0.034 2.00e-02 2.50e+03 3.43e-02 1.47e+01 pdb=" CG ASN A 97 " 0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN A 97 " 0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN A 97 " 0.051 2.00e-02 2.50e+03 pdb=" C1 NAG D 1 " -0.041 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN B 97 " 0.034 2.00e-02 2.50e+03 3.42e-02 1.46e+01 pdb=" CG ASN B 97 " -0.019 2.00e-02 2.50e+03 pdb=" OD1 ASN B 97 " -0.006 2.00e-02 2.50e+03 pdb=" ND2 ASN B 97 " -0.051 2.00e-02 2.50e+03 pdb=" C1 NAG F 1 " 0.041 2.00e-02 2.50e+03 ... (remaining 2058 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.92: 5075 2.92 - 3.42: 10525 3.42 - 3.91: 20377 3.91 - 4.41: 22896 4.41 - 4.90: 37998 Nonbonded interactions: 96871 Sorted by model distance: nonbonded pdb=" OD2 ASP C 137 " pdb=" NZ LYS C 139A" model vdw 2.426 3.120 nonbonded pdb=" OD2 ASP B 137 " pdb=" NZ LYS B 139A" model vdw 2.426 3.120 nonbonded pdb=" OD2 ASP A 137 " pdb=" NZ LYS A 139A" model vdw 2.427 3.120 nonbonded pdb=" O ASN B 269 " pdb=" N GLY B 271 " model vdw 2.532 3.120 nonbonded pdb=" O ASN C 269 " pdb=" N GLY C 271 " model vdw 2.532 3.120 ... (remaining 96866 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 11 through 659 or (resid 660 through 662 and (name N or na \ me CA or name C or name O or name CB )) or resid 663 through 904)) selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.000 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 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:1.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 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 : 0.016 0.100 11902 Z= 0.884 Angle : 1.492 30.918 16213 Z= 0.930 Chirality : 0.098 0.671 1836 Planarity : 0.006 0.031 2043 Dihedral : 10.152 81.791 4123 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 0.40 Ramachandran Plot: Outliers : 0.21 % Allowed : 1.88 % Favored : 97.91 % Rotamer: Outliers : 0.50 % Allowed : 0.76 % Favored : 98.74 % 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: 0.26 (0.19), residues: 1437 helix: 0.11 (0.23), residues: 375 sheet: 1.10 (0.30), residues: 258 loop : -0.01 (0.19), residues: 804 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 599 TYR 0.035 0.006 TYR B 587 PHE 0.023 0.004 PHE C 209 TRP 0.017 0.004 TRP A 133 HIS 0.004 0.001 HIS C 635 Details of bonding type rmsd/Z covalent geometry : bond 0.01593 / 0.87 (11860) covalent geometry : angle 1.47213 / 0.93 (16105) SS BOND : bond 0.01400 / 0.82 ( 18) SS BOND : angle 3.93858 / 2.39 ( 36) hydrogen bonds : bond 0.15912 / 11.29 ( 468) hydrogen bonds : angle 7.59117 / 5.49 ( 1368) link_BETA1-4 : bond 0.07257 / 4.31 ( 6) link_BETA1-4 : angle 4.16596 / 2.48 ( 18) link_NAG-ASN : bond 0.06944 / 4.65 ( 18) link_NAG-ASN : angle 2.45076 / 1.54 ( 54) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 139 time to evaluate : 0.445 Fit side-chains REVERT: C 104 ASP cc_start: 0.6936 (m-30) cc_final: 0.6733 (m-30) outliers start: 6 outliers final: 3 residues processed: 145 average time/residue: 0.1267 time to fit residues: 25.1746 Evaluate side-chains 56 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ASN Chi-restraints excluded: chain B residue 33 ASN Chi-restraints excluded: chain C residue 33 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 0.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.117631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.095277 restraints weight = 18989.742| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.55 r_work: 0.3068 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3068 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 11902 Z= 0.158 Angle : 0.611 6.590 16213 Z= 0.322 Chirality : 0.046 0.276 1836 Planarity : 0.004 0.040 2043 Dihedral : 4.555 21.244 1563 Min Nonbonded Distance : 2.593 Molprobity Statistics. All-atom Clashscore : 2.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.17 % Allowed : 3.86 % Favored : 94.97 % 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: 0.85 (0.20), residues: 1437 helix: 1.60 (0.26), residues: 357 sheet: 0.62 (0.29), residues: 288 loop : 0.16 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 599 TYR 0.024 0.002 TYR A 650 PHE 0.016 0.002 PHE B 631 TRP 0.009 0.001 TRP B 514 HIS 0.003 0.001 HIS C 635 Details of bonding type rmsd/Z covalent geometry : bond 0.00349 / 0.16 (11860) covalent geometry : angle 0.59077 / 0.32 (16105) SS BOND : bond 0.00446 / 0.29 ( 18) SS BOND : angle 1.39847 / 0.81 ( 36) hydrogen bonds : bond 0.05272 / 3.73 ( 468) hydrogen bonds : angle 5.49184 / 3.96 ( 1368) link_BETA1-4 : bond 0.00177 / 0.11 ( 6) link_BETA1-4 : angle 1.52345 / 0.86 ( 18) link_NAG-ASN : bond 0.00443 / 0.29 ( 18) link_NAG-ASN : angle 2.42239 / 1.46 ( 54) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8379 (pp-130) cc_final: 0.7656 (ptt) REVERT: B 266 MET cc_start: 0.8345 (pp-130) cc_final: 0.7586 (ptt) REVERT: C 104 ASP cc_start: 0.7679 (m-30) cc_final: 0.7433 (m-30) REVERT: C 110 GLU cc_start: 0.8232 (mm-30) cc_final: 0.8028 (mm-30) REVERT: C 266 MET cc_start: 0.8397 (pp-130) cc_final: 0.7745 (ptt) REVERT: C 595 LEU cc_start: 0.8124 (OUTLIER) cc_final: 0.7570 (mp) outliers start: 14 outliers final: 4 residues processed: 81 average time/residue: 0.1006 time to fit residues: 12.3224 Evaluate side-chains 45 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 216 SER Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 216 SER Chi-restraints excluded: chain C residue 595 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 4.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 6.9990 chunk 128 optimal weight: 0.4980 chunk 34 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 555 GLN B 555 GLN C 555 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.112989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.090191 restraints weight = 19325.682| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 2.57 r_work: 0.2983 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11902 Z= 0.223 Angle : 0.618 12.204 16213 Z= 0.314 Chirality : 0.046 0.230 1836 Planarity : 0.004 0.074 2043 Dihedral : 4.295 24.414 1557 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.01 % Allowed : 5.79 % Favored : 93.20 % 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: 0.41 (0.21), residues: 1437 helix: 1.34 (0.27), residues: 378 sheet: 0.04 (0.30), residues: 294 loop : -0.09 (0.20), residues: 765 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 599 TYR 0.027 0.002 TYR A 650 PHE 0.013 0.002 PHE C 127 TRP 0.008 0.001 TRP B 159 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00522 / 0.22 (11860) covalent geometry : angle 0.57937 / 0.31 (16105) SS BOND : bond 0.00342 / 0.23 ( 18) SS BOND : angle 1.54748 / 0.93 ( 36) hydrogen bonds : bond 0.04701 / 3.34 ( 468) hydrogen bonds : angle 5.22330 / 3.76 ( 1368) link_BETA1-4 : bond 0.00309 / 0.19 ( 6) link_BETA1-4 : angle 1.15670 / 0.72 ( 18) link_NAG-ASN : bond 0.01136 / 0.73 ( 18) link_NAG-ASN : angle 3.52591 / 2.23 ( 54) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.466 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8223 (ptt) REVERT: A 531 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.8002 (tt) REVERT: B 266 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.7791 (ptt) REVERT: C 104 ASP cc_start: 0.7753 (m-30) cc_final: 0.7490 (m-30) REVERT: C 266 MET cc_start: 0.8543 (OUTLIER) cc_final: 0.8011 (ptt) REVERT: C 595 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7814 (mp) REVERT: C 650 TYR cc_start: 0.7407 (t80) cc_final: 0.7196 (t80) outliers start: 12 outliers final: 4 residues processed: 51 average time/residue: 0.0704 time to fit residues: 6.3427 Evaluate side-chains 45 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 36 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Chi-restraints excluded: chain C residue 595 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 78 optimal weight: 0.0470 chunk 129 optimal weight: 4.9990 chunk 85 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 3 optimal weight: 0.6980 chunk 97 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 136 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 18 HIS C 18 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.092717 restraints weight = 19074.441| |-----------------------------------------------------------------------------| r_work (start): 0.3173 rms_B_bonded: 2.51 r_work: 0.3019 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3019 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 11902 Z= 0.118 Angle : 0.527 12.641 16213 Z= 0.263 Chirality : 0.043 0.260 1836 Planarity : 0.004 0.037 2043 Dihedral : 3.893 19.795 1557 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.92 % Allowed : 6.12 % Favored : 92.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.22), residues: 1437 helix: 1.72 (0.27), residues: 375 sheet: 0.05 (0.33), residues: 264 loop : 0.01 (0.21), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 599 TYR 0.022 0.001 TYR B 650 PHE 0.012 0.001 PHE A 631 TRP 0.005 0.001 TRP B 514 HIS 0.003 0.000 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (11860) covalent geometry : angle 0.47924 / 0.25 (16105) SS BOND : bond 0.00226 / 0.15 ( 18) SS BOND : angle 0.90196 / 0.54 ( 36) hydrogen bonds : bond 0.04060 / 2.88 ( 468) hydrogen bonds : angle 4.91535 / 3.54 ( 1368) link_BETA1-4 : bond 0.00351 / 0.21 ( 6) link_BETA1-4 : angle 1.02386 / 0.64 ( 18) link_NAG-ASN : bond 0.00982 / 0.63 ( 18) link_NAG-ASN : angle 3.72913 / 2.35 ( 54) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.449 Fit side-chains REVERT: A 110 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8122 (mm-30) REVERT: A 266 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7770 (ptt) REVERT: B 266 MET cc_start: 0.8244 (OUTLIER) cc_final: 0.7862 (ptt) REVERT: C 266 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7866 (ptt) outliers start: 11 outliers final: 1 residues processed: 59 average time/residue: 0.0760 time to fit residues: 7.4253 Evaluate side-chains 43 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 chunk 139 optimal weight: 5.9990 chunk 110 optimal weight: 0.0040 chunk 69 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.112061 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.089512 restraints weight = 19274.998| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.50 r_work: 0.2966 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8468 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 11902 Z= 0.202 Angle : 0.581 12.832 16213 Z= 0.289 Chirality : 0.045 0.257 1836 Planarity : 0.004 0.038 2043 Dihedral : 4.038 27.136 1557 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 1.51 % Allowed : 5.87 % Favored : 92.62 % 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: 0.41 (0.22), residues: 1437 helix: 1.74 (0.27), residues: 375 sheet: -0.18 (0.30), residues: 300 loop : -0.22 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 112 TYR 0.024 0.002 TYR C 650 PHE 0.010 0.001 PHE C 105 TRP 0.007 0.001 TRP C 159 HIS 0.007 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00478 / 0.20 (11860) covalent geometry : angle 0.53267 / 0.28 (16105) SS BOND : bond 0.00336 / 0.22 ( 18) SS BOND : angle 1.52608 / 0.89 ( 36) hydrogen bonds : bond 0.04174 / 2.98 ( 468) hydrogen bonds : angle 4.99534 / 3.60 ( 1368) link_BETA1-4 : bond 0.00219 / 0.14 ( 6) link_BETA1-4 : angle 1.12609 / 0.70 ( 18) link_NAG-ASN : bond 0.00885 / 0.56 ( 18) link_NAG-ASN : angle 3.83502 / 2.40 ( 54) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 44 time to evaluate : 0.491 Fit side-chains REVERT: A 110 GLU cc_start: 0.8438 (mm-30) cc_final: 0.8116 (mm-30) REVERT: A 266 MET cc_start: 0.8523 (OUTLIER) cc_final: 0.7855 (ptt) REVERT: B 266 MET cc_start: 0.8414 (OUTLIER) cc_final: 0.8029 (ptt) REVERT: C 266 MET cc_start: 0.8508 (OUTLIER) cc_final: 0.8054 (ptt) outliers start: 18 outliers final: 9 residues processed: 55 average time/residue: 0.0697 time to fit residues: 6.7936 Evaluate side-chains 50 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 38 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 138 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 chunk 18 optimal weight: 6.9990 chunk 90 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.111702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.089340 restraints weight = 19300.639| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 2.50 r_work: 0.2952 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 11902 Z= 0.207 Angle : 0.573 12.829 16213 Z= 0.285 Chirality : 0.045 0.250 1836 Planarity : 0.004 0.035 2043 Dihedral : 3.987 23.910 1557 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 0.92 % Allowed : 7.38 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.20 (0.21), residues: 1437 helix: 1.76 (0.27), residues: 375 sheet: -0.69 (0.31), residues: 243 loop : -0.32 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 112 TYR 0.025 0.002 TYR C 650 PHE 0.009 0.001 PHE A 121 TRP 0.005 0.001 TRP C 159 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00488 / 0.21 (11860) covalent geometry : angle 0.52388 / 0.27 (16105) SS BOND : bond 0.00335 / 0.22 ( 18) SS BOND : angle 1.52402 / 0.89 ( 36) hydrogen bonds : bond 0.04089 / 2.92 ( 468) hydrogen bonds : angle 4.99018 / 3.60 ( 1368) link_BETA1-4 : bond 0.00261 / 0.15 ( 6) link_BETA1-4 : angle 1.06625 / 0.66 ( 18) link_NAG-ASN : bond 0.00846 / 0.54 ( 18) link_NAG-ASN : angle 3.86787 / 2.42 ( 54) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.449 Fit side-chains REVERT: A 110 GLU cc_start: 0.8419 (mm-30) cc_final: 0.8111 (mm-30) REVERT: A 266 MET cc_start: 0.8529 (OUTLIER) cc_final: 0.7906 (ptt) REVERT: B 266 MET cc_start: 0.8488 (OUTLIER) cc_final: 0.8117 (ptt) REVERT: C 266 MET cc_start: 0.8544 (OUTLIER) cc_final: 0.8103 (ptt) outliers start: 11 outliers final: 7 residues processed: 46 average time/residue: 0.0917 time to fit residues: 6.9822 Evaluate side-chains 47 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 37 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain A residue 595 LEU Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 0.9980 chunk 79 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 96 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 5.9990 chunk 127 optimal weight: 0.9980 chunk 47 optimal weight: 0.2980 chunk 118 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 4.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 18 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.112514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.089539 restraints weight = 19183.286| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.59 r_work: 0.2968 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2968 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11902 Z= 0.144 Angle : 0.528 12.774 16213 Z= 0.262 Chirality : 0.044 0.248 1836 Planarity : 0.003 0.037 2043 Dihedral : 3.789 21.332 1557 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.67 % Allowed : 7.63 % Favored : 91.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.38 (0.22), residues: 1437 helix: 1.93 (0.27), residues: 381 sheet: -0.87 (0.34), residues: 213 loop : -0.18 (0.20), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 599 TYR 0.021 0.001 TYR C 650 PHE 0.008 0.001 PHE B 121 TRP 0.005 0.001 TRP B 514 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (11860) covalent geometry : angle 0.47847 / 0.25 (16105) SS BOND : bond 0.00272 / 0.18 ( 18) SS BOND : angle 0.99277 / 0.59 ( 36) hydrogen bonds : bond 0.03849 / 2.75 ( 468) hydrogen bonds : angle 4.82887 / 3.49 ( 1368) link_BETA1-4 : bond 0.00284 / 0.17 ( 6) link_BETA1-4 : angle 0.99258 / 0.62 ( 18) link_NAG-ASN : bond 0.00841 / 0.54 ( 18) link_NAG-ASN : angle 3.81039 / 2.39 ( 54) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 44 time to evaluate : 0.397 Fit side-chains REVERT: A 110 GLU cc_start: 0.8398 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 266 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.7898 (ptt) REVERT: B 266 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8097 (ptt) REVERT: B 626 ILE cc_start: 0.7975 (pt) cc_final: 0.7671 (mp) REVERT: C 266 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.8032 (ptt) outliers start: 8 outliers final: 5 residues processed: 48 average time/residue: 0.0768 time to fit residues: 6.4884 Evaluate side-chains 47 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 39 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 90 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 10.0000 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 70 optimal weight: 2.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.109779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.086520 restraints weight = 19631.497| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.61 r_work: 0.2912 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.3490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 11902 Z= 0.288 Angle : 0.617 13.048 16213 Z= 0.305 Chirality : 0.047 0.268 1836 Planarity : 0.004 0.035 2043 Dihedral : 4.074 22.260 1557 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 1.09 % Allowed : 7.55 % Favored : 91.36 % 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: 0.09 (0.21), residues: 1437 helix: 1.72 (0.27), residues: 381 sheet: -0.82 (0.31), residues: 243 loop : -0.41 (0.20), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 123 TYR 0.019 0.002 TYR C 650 PHE 0.011 0.002 PHE C 105 TRP 0.007 0.001 TRP C 159 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00684 / 0.29 (11860) covalent geometry : angle 0.57014 / 0.29 (16105) SS BOND : bond 0.00402 / 0.27 ( 18) SS BOND : angle 1.26406 / 0.75 ( 36) hydrogen bonds : bond 0.04221 / 3.02 ( 468) hydrogen bonds : angle 5.08118 / 3.66 ( 1368) link_BETA1-4 : bond 0.00209 / 0.12 ( 6) link_BETA1-4 : angle 1.13163 / 0.68 ( 18) link_NAG-ASN : bond 0.00843 / 0.54 ( 18) link_NAG-ASN : angle 3.97027 / 2.48 ( 54) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.511 Fit side-chains REVERT: A 110 GLU cc_start: 0.8477 (mm-30) cc_final: 0.8162 (mm-30) REVERT: A 266 MET cc_start: 0.8568 (OUTLIER) cc_final: 0.7969 (ptt) REVERT: B 266 MET cc_start: 0.8602 (OUTLIER) cc_final: 0.8219 (ptt) REVERT: B 626 ILE cc_start: 0.8125 (pt) cc_final: 0.7797 (mp) REVERT: C 266 MET cc_start: 0.8641 (OUTLIER) cc_final: 0.8163 (ptt) REVERT: C 626 ILE cc_start: 0.8008 (pt) cc_final: 0.7718 (mp) outliers start: 13 outliers final: 6 residues processed: 51 average time/residue: 0.0737 time to fit residues: 6.4628 Evaluate side-chains 51 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain A residue 531 LEU Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 531 LEU Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 89 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 109 optimal weight: 0.9990 chunk 76 optimal weight: 0.9990 chunk 138 optimal weight: 0.7980 chunk 103 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.112650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.089555 restraints weight = 19080.816| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 2.57 r_work: 0.2960 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11902 Z= 0.137 Angle : 0.537 12.742 16213 Z= 0.266 Chirality : 0.044 0.248 1836 Planarity : 0.003 0.040 2043 Dihedral : 3.869 25.509 1557 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.84 % Allowed : 7.89 % Favored : 91.28 % 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: 0.27 (0.22), residues: 1437 helix: 1.85 (0.27), residues: 384 sheet: -0.99 (0.34), residues: 213 loop : -0.23 (0.20), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.019 0.001 TYR C 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 585 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 (11860) covalent geometry : angle 0.48713 / 0.26 (16105) SS BOND : bond 0.00264 / 0.18 ( 18) SS BOND : angle 1.10959 / 0.67 ( 36) hydrogen bonds : bond 0.03822 / 2.72 ( 468) hydrogen bonds : angle 4.83880 / 3.49 ( 1368) link_BETA1-4 : bond 0.00302 / 0.18 ( 6) link_BETA1-4 : angle 0.95588 / 0.60 ( 18) link_NAG-ASN : bond 0.00823 / 0.53 ( 18) link_NAG-ASN : angle 3.81977 / 2.39 ( 54) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.428 Fit side-chains REVERT: A 110 GLU cc_start: 0.8389 (mm-30) cc_final: 0.8075 (mm-30) REVERT: A 266 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.7961 (ptt) REVERT: B 266 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8131 (ptt) REVERT: C 266 MET cc_start: 0.8521 (OUTLIER) cc_final: 0.8148 (ptt) REVERT: C 626 ILE cc_start: 0.7976 (pt) cc_final: 0.7672 (mp) outliers start: 10 outliers final: 6 residues processed: 48 average time/residue: 0.0613 time to fit residues: 5.2854 Evaluate side-chains 50 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 109 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 92 optimal weight: 9.9990 chunk 107 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.112885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.089942 restraints weight = 19241.113| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 2.58 r_work: 0.2966 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.3592 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11902 Z= 0.134 Angle : 0.535 12.757 16213 Z= 0.265 Chirality : 0.044 0.251 1836 Planarity : 0.004 0.040 2043 Dihedral : 3.817 24.042 1557 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.76 % Allowed : 7.72 % Favored : 91.53 % 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: 0.35 (0.22), residues: 1437 helix: 1.92 (0.27), residues: 384 sheet: -0.96 (0.35), residues: 213 loop : -0.19 (0.21), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.019 0.001 TYR C 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 514 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (11860) covalent geometry : angle 0.48452 / 0.25 (16105) SS BOND : bond 0.00245 / 0.16 ( 18) SS BOND : angle 1.35158 / 0.83 ( 36) hydrogen bonds : bond 0.03758 / 2.68 ( 468) hydrogen bonds : angle 4.77155 / 3.44 ( 1368) link_BETA1-4 : bond 0.00287 / 0.17 ( 6) link_BETA1-4 : angle 0.97985 / 0.61 ( 18) link_NAG-ASN : bond 0.00830 / 0.53 ( 18) link_NAG-ASN : angle 3.80571 / 2.39 ( 54) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2874 Ramachandran restraints generated. 1437 Oldfield, 0 Emsley, 1437 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.476 Fit side-chains REVERT: A 110 GLU cc_start: 0.8383 (mm-30) cc_final: 0.8068 (mm-30) REVERT: A 266 MET cc_start: 0.8391 (OUTLIER) cc_final: 0.7907 (ptt) REVERT: B 266 MET cc_start: 0.8451 (OUTLIER) cc_final: 0.8112 (ptt) REVERT: C 266 MET cc_start: 0.8431 (OUTLIER) cc_final: 0.8062 (ptt) REVERT: C 626 ILE cc_start: 0.7999 (pt) cc_final: 0.7680 (mp) outliers start: 9 outliers final: 6 residues processed: 47 average time/residue: 0.0928 time to fit residues: 7.0729 Evaluate side-chains 50 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 200 LEU Chi-restraints excluded: chain A residue 266 MET Chi-restraints excluded: chain B residue 25 THR Chi-restraints excluded: chain B residue 57 VAL Chi-restraints excluded: chain B residue 266 MET Chi-restraints excluded: chain B residue 595 LEU Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 266 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 6 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 109 optimal weight: 0.4980 chunk 121 optimal weight: 0.3980 chunk 142 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 101 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.113148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.089896 restraints weight = 19185.131| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 2.62 r_work: 0.2967 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11902 Z= 0.135 Angle : 0.530 12.766 16213 Z= 0.262 Chirality : 0.044 0.252 1836 Planarity : 0.003 0.037 2043 Dihedral : 3.756 23.251 1557 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 0.84 % Allowed : 7.63 % Favored : 91.53 % 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: 0.39 (0.22), residues: 1437 helix: 2.03 (0.27), residues: 381 sheet: -0.97 (0.35), residues: 213 loop : -0.19 (0.21), residues: 843 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 112 TYR 0.020 0.001 TYR C 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 585 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.13 (11860) covalent geometry : angle 0.47979 / 0.25 (16105) SS BOND : bond 0.00228 / 0.15 ( 18) SS BOND : angle 1.15941 / 0.71 ( 36) hydrogen bonds : bond 0.03695 / 2.64 ( 468) hydrogen bonds : angle 4.72901 / 3.41 ( 1368) link_BETA1-4 : bond 0.00284 / 0.17 ( 6) link_BETA1-4 : angle 0.96772 / 0.61 ( 18) link_NAG-ASN : bond 0.00824 / 0.53 ( 18) link_NAG-ASN : angle 3.79391 / 2.38 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1930.31 seconds wall clock time: 34 minutes 17.59 seconds (2057.59 seconds total)