Starting phenix.real_space_refine on Wed Mar 4 06:46:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7kna_22937/03_2026/7kna_22937.cif Found real_map, /net/cci-nas-00/data/ceres_data/7kna_22937/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7kna_22937/03_2026/7kna_22937.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7kna_22937/03_2026/7kna_22937.map" model { file = "/net/cci-nas-00/data/ceres_data/7kna_22937/03_2026/7kna_22937.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7kna_22937/03_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-5986/lib/python3.9/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 dihedrals: 6 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 dihedrals: 6 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 dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 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: "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 dihedrals: 12 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 dihedrals: 12 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 dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 2.71, per 1000 atoms: 0.23 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: 0.77 Conformation dependent library (CDL) restraints added in 441.9 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: 0.29 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: 1.69 Time building geometry restraints manager: 1.04 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: 7000 16.36 - 32.72: 288 32.72 - 49.07: 48 49.07 - 65.43: 30 65.43 - 81.79: 9 Dihedral angle restraints: 7375 sinusoidal: 3169 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 7372 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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 10.650 Find NCS groups from input model: 0.210 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:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 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 : 10.095 81.791 4627 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 covalent geometry : bond 0.01593 (11860) covalent geometry : angle 1.47213 (16105) SS BOND : bond 0.01400 ( 18) SS BOND : angle 3.93858 ( 36) hydrogen bonds : bond 0.15912 ( 468) hydrogen bonds : angle 7.59117 ( 1368) link_BETA1-4 : bond 0.07257 ( 6) link_BETA1-4 : angle 4.16596 ( 18) link_NAG-ASN : bond 0.06944 ( 18) link_NAG-ASN : angle 2.45076 ( 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 : 0.434 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: 0.1374 time to fit residues: 27.0561 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 : 0.435 ------------------------------------------------------------------------------- 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: 0.6980 chunk 77 optimal weight: 2.9990 chunk 122 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.117931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.095650 restraints weight = 18966.928| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 2.54 r_work: 0.3072 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3072 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11902 Z= 0.158 Angle : 0.614 6.706 16213 Z= 0.324 Chirality : 0.046 0.295 1836 Planarity : 0.004 0.035 2043 Dihedral : 5.255 30.992 2067 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 0.84 % Allowed : 4.03 % Favored : 95.13 % 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: 0.89 (0.20), residues: 1437 helix: 1.66 (0.26), residues: 357 sheet: 0.67 (0.29), residues: 288 loop : 0.14 (0.20), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 599 TYR 0.023 0.002 TYR A 650 PHE 0.015 0.002 PHE B 631 TRP 0.009 0.001 TRP B 514 HIS 0.004 0.001 HIS C 635 Details of bonding type rmsd covalent geometry : bond 0.00344 (11860) covalent geometry : angle 0.59193 (16105) SS BOND : bond 0.00642 ( 18) SS BOND : angle 1.51673 ( 36) hydrogen bonds : bond 0.05491 ( 468) hydrogen bonds : angle 5.52751 ( 1368) link_BETA1-4 : bond 0.00150 ( 6) link_BETA1-4 : angle 1.59138 ( 18) link_NAG-ASN : bond 0.00555 ( 18) link_NAG-ASN : angle 2.52863 ( 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 78 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.417 Fit side-chains revert: symmetry clash REVERT: A 266 MET cc_start: 0.8394 (pp-130) cc_final: 0.7636 (ptt) REVERT: B 266 MET cc_start: 0.8311 (pp-130) cc_final: 0.7542 (ptt) REVERT: C 104 ASP cc_start: 0.7679 (m-30) cc_final: 0.7432 (m-30) REVERT: C 266 MET cc_start: 0.8396 (pp-130) cc_final: 0.7716 (ptt) REVERT: C 595 LEU cc_start: 0.8086 (OUTLIER) cc_final: 0.7576 (mp) outliers start: 10 outliers final: 3 residues processed: 77 average time/residue: 0.1182 time to fit residues: 13.3789 Evaluate side-chains 44 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 48 optimal weight: 8.9990 chunk 87 optimal weight: 2.9990 chunk 126 optimal weight: 2.9990 chunk 10 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 0.0060 chunk 75 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 HIS A 555 GLN B 18 HIS B 555 GLN C 18 HIS C 555 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.111459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.088326 restraints weight = 19577.286| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.62 r_work: 0.2942 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.091 11902 Z= 0.285 Angle : 0.647 6.200 16213 Z= 0.336 Chirality : 0.048 0.237 1836 Planarity : 0.004 0.062 2043 Dihedral : 5.086 28.692 2061 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.34 % Allowed : 5.87 % Favored : 92.79 % 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: 0.32 (0.21), residues: 1437 helix: 1.19 (0.26), residues: 378 sheet: -0.02 (0.29), residues: 300 loop : -0.10 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 599 TYR 0.026 0.002 TYR A 650 PHE 0.016 0.002 PHE C 127 TRP 0.010 0.002 TRP B 159 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00678 (11860) covalent geometry : angle 0.62461 (16105) SS BOND : bond 0.00612 ( 18) SS BOND : angle 1.86352 ( 36) hydrogen bonds : bond 0.04882 ( 468) hydrogen bonds : angle 5.39267 ( 1368) link_BETA1-4 : bond 0.00374 ( 6) link_BETA1-4 : angle 1.43011 ( 18) link_NAG-ASN : bond 0.00513 ( 18) link_NAG-ASN : angle 2.50424 ( 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 61 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.454 Fit side-chains REVERT: A 266 MET cc_start: 0.8609 (OUTLIER) cc_final: 0.8313 (ptt) REVERT: B 266 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8018 (ptt) REVERT: C 104 ASP cc_start: 0.7847 (m-30) cc_final: 0.7583 (m-30) REVERT: C 266 MET cc_start: 0.8569 (OUTLIER) cc_final: 0.8029 (ptt) REVERT: C 595 LEU cc_start: 0.8274 (OUTLIER) cc_final: 0.7918 (mp) outliers start: 16 outliers final: 6 residues processed: 56 average time/residue: 0.0745 time to fit residues: 7.3334 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 : 0.464 ------------------------------------------------------------------------------- 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 275 ILE 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: 0.9990 chunk 129 optimal weight: 0.8980 chunk 85 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 3 optimal weight: 0.4980 chunk 97 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 0.7980 chunk 136 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.114048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.091455 restraints weight = 19189.562| |-----------------------------------------------------------------------------| r_work (start): 0.3153 rms_B_bonded: 2.51 r_work: 0.3000 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11902 Z= 0.128 Angle : 0.559 13.834 16213 Z= 0.277 Chirality : 0.044 0.288 1836 Planarity : 0.004 0.037 2043 Dihedral : 5.300 52.269 2061 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 1.26 % Allowed : 5.96 % Favored : 92.79 % 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: 0.44 (0.21), residues: 1437 helix: 1.56 (0.27), residues: 375 sheet: -0.07 (0.30), residues: 300 loop : -0.12 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 599 TYR 0.024 0.001 TYR C 650 PHE 0.012 0.001 PHE A 631 TRP 0.006 0.001 TRP C 514 HIS 0.005 0.001 HIS A 18 Details of bonding type rmsd covalent geometry : bond 0.00284 (11860) covalent geometry : angle 0.50524 (16105) SS BOND : bond 0.00241 ( 18) SS BOND : angle 0.94347 ( 36) hydrogen bonds : bond 0.04268 ( 468) hydrogen bonds : angle 5.05439 ( 1368) link_BETA1-4 : bond 0.00367 ( 6) link_BETA1-4 : angle 1.13572 ( 18) link_NAG-ASN : bond 0.00842 ( 18) link_NAG-ASN : angle 4.06717 ( 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 59 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.457 Fit side-chains REVERT: A 110 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8145 (mm-30) REVERT: A 266 MET cc_start: 0.8476 (OUTLIER) cc_final: 0.7861 (ptt) REVERT: B 266 MET cc_start: 0.8349 (OUTLIER) cc_final: 0.7941 (ptt) REVERT: C 266 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.7988 (ptt) outliers start: 15 outliers final: 5 residues processed: 53 average time/residue: 0.0866 time to fit residues: 7.6402 Evaluate side-chains 49 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 41 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 89 optimal weight: 3.9990 chunk 60 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 90 optimal weight: 1.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 69 optimal weight: 0.9990 chunk 105 optimal weight: 0.0980 chunk 53 optimal weight: 4.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.114390 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.091567 restraints weight = 19038.626| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 2.56 r_work: 0.2994 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2994 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.2887 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11902 Z= 0.126 Angle : 0.531 12.715 16213 Z= 0.265 Chirality : 0.043 0.254 1836 Planarity : 0.004 0.036 2043 Dihedral : 4.665 34.359 2061 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.26 % Allowed : 5.96 % Favored : 92.79 % 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: 0.48 (0.22), residues: 1437 helix: 1.79 (0.27), residues: 375 sheet: -0.13 (0.30), residues: 300 loop : -0.16 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 599 TYR 0.025 0.001 TYR C 650 PHE 0.008 0.001 PHE B 121 TRP 0.005 0.001 TRP C 159 HIS 0.004 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00285 (11860) covalent geometry : angle 0.48027 (16105) SS BOND : bond 0.00243 ( 18) SS BOND : angle 1.22786 ( 36) hydrogen bonds : bond 0.03977 ( 468) hydrogen bonds : angle 4.86976 ( 1368) link_BETA1-4 : bond 0.00319 ( 6) link_BETA1-4 : angle 1.13453 ( 18) link_NAG-ASN : bond 0.00938 ( 18) link_NAG-ASN : angle 3.80747 ( 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 66 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 51 time to evaluate : 0.464 Fit side-chains REVERT: A 110 GLU cc_start: 0.8407 (mm-30) cc_final: 0.8085 (mm-30) REVERT: A 266 MET cc_start: 0.8426 (OUTLIER) cc_final: 0.7853 (ptt) REVERT: B 266 MET cc_start: 0.8332 (OUTLIER) cc_final: 0.7997 (ptt) REVERT: C 266 MET cc_start: 0.8398 (OUTLIER) cc_final: 0.7972 (ptt) outliers start: 15 outliers final: 5 residues processed: 59 average time/residue: 0.0757 time to fit residues: 7.8636 Evaluate side-chains 50 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 266 MET 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 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: 2.9990 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 65 optimal weight: 0.6980 chunk 104 optimal weight: 8.9990 chunk 15 optimal weight: 0.0370 chunk 111 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 90 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 overall best weight: 1.4862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.111898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.089006 restraints weight = 19262.166| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.57 r_work: 0.2952 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11902 Z= 0.191 Angle : 0.562 12.549 16213 Z= 0.279 Chirality : 0.045 0.262 1836 Planarity : 0.004 0.035 2043 Dihedral : 4.614 31.145 2061 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 1.34 % Allowed : 6.63 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.79 (0.27), residues: 375 sheet: -0.32 (0.30), residues: 300 loop : -0.22 (0.21), residues: 762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 112 TYR 0.025 0.002 TYR C 650 PHE 0.009 0.001 PHE C 105 TRP 0.006 0.001 TRP C 159 HIS 0.005 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00451 (11860) covalent geometry : angle 0.51262 (16105) SS BOND : bond 0.00391 ( 18) SS BOND : angle 1.41176 ( 36) hydrogen bonds : bond 0.04076 ( 468) hydrogen bonds : angle 4.95128 ( 1368) link_BETA1-4 : bond 0.00266 ( 6) link_BETA1-4 : angle 1.25465 ( 18) link_NAG-ASN : bond 0.00861 ( 18) link_NAG-ASN : angle 3.83133 ( 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 59 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.486 Fit side-chains REVERT: A 110 GLU cc_start: 0.8443 (mm-30) cc_final: 0.8144 (mm-30) REVERT: A 266 MET cc_start: 0.8510 (OUTLIER) cc_final: 0.7913 (ptt) REVERT: B 266 MET cc_start: 0.8430 (OUTLIER) cc_final: 0.8086 (ptt) REVERT: C 110 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7877 (mm-30) REVERT: C 266 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8077 (ptt) outliers start: 16 outliers final: 8 residues processed: 53 average time/residue: 0.0769 time to fit residues: 7.2098 Evaluate side-chains 55 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.447 ------------------------------------------------------------------------------- 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 84 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 87 optimal weight: 2.9990 chunk 96 optimal weight: 10.0000 chunk 10 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 chunk 127 optimal weight: 7.9990 chunk 47 optimal weight: 10.0000 chunk 118 optimal weight: 0.9990 chunk 14 optimal weight: 3.9990 chunk 141 optimal weight: 2.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.110103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.087185 restraints weight = 19460.994| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 2.56 r_work: 0.2926 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 11902 Z= 0.256 Angle : 0.607 12.958 16213 Z= 0.301 Chirality : 0.046 0.271 1836 Planarity : 0.004 0.035 2043 Dihedral : 5.228 38.854 2061 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.17 % Allowed : 7.21 % Favored : 91.61 % 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: 0.14 (0.21), residues: 1437 helix: 1.71 (0.27), residues: 375 sheet: -0.78 (0.31), residues: 243 loop : -0.35 (0.20), residues: 819 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 123 TYR 0.022 0.002 TYR A 650 PHE 0.011 0.002 PHE C 105 TRP 0.006 0.001 TRP C 159 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00607 (11860) covalent geometry : angle 0.55681 (16105) SS BOND : bond 0.00377 ( 18) SS BOND : angle 1.53395 ( 36) hydrogen bonds : bond 0.04239 ( 468) hydrogen bonds : angle 5.09448 ( 1368) link_BETA1-4 : bond 0.00242 ( 6) link_BETA1-4 : angle 1.31234 ( 18) link_NAG-ASN : bond 0.00847 ( 18) link_NAG-ASN : angle 3.99705 ( 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 60 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.353 Fit side-chains REVERT: A 110 GLU cc_start: 0.8453 (mm-30) cc_final: 0.8138 (mm-30) REVERT: A 266 MET cc_start: 0.8604 (OUTLIER) cc_final: 0.7956 (ptt) REVERT: B 266 MET cc_start: 0.8599 (OUTLIER) cc_final: 0.8201 (ptt) REVERT: B 626 ILE cc_start: 0.8149 (pt) cc_final: 0.7835 (mp) REVERT: C 266 MET cc_start: 0.8625 (OUTLIER) cc_final: 0.8143 (ptt) REVERT: C 626 ILE cc_start: 0.8033 (pt) cc_final: 0.7752 (mp) outliers start: 14 outliers final: 9 residues processed: 55 average time/residue: 0.0903 time to fit residues: 8.0463 Evaluate side-chains 55 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.500 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 106 optimal weight: 1.9990 chunk 142 optimal weight: 10.0000 chunk 90 optimal weight: 0.8980 chunk 111 optimal weight: 2.9990 chunk 108 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 8.9990 chunk 117 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 70 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.111411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.088405 restraints weight = 19402.759| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.59 r_work: 0.2943 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 11902 Z= 0.177 Angle : 0.552 12.808 16213 Z= 0.273 Chirality : 0.044 0.259 1836 Planarity : 0.004 0.037 2043 Dihedral : 5.151 41.217 2061 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.84 % Allowed : 7.97 % Favored : 91.19 % 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: 0.21 (0.22), residues: 1437 helix: 1.80 (0.27), residues: 381 sheet: -0.79 (0.32), residues: 243 loop : -0.32 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.021 0.002 TYR A 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 585 HIS 0.006 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00415 (11860) covalent geometry : angle 0.50126 (16105) SS BOND : bond 0.00321 ( 18) SS BOND : angle 1.10332 ( 36) hydrogen bonds : bond 0.03951 ( 468) hydrogen bonds : angle 4.92459 ( 1368) link_BETA1-4 : bond 0.00337 ( 6) link_BETA1-4 : angle 1.11372 ( 18) link_NAG-ASN : bond 0.00812 ( 18) link_NAG-ASN : angle 3.90728 ( 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 55 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.466 Fit side-chains REVERT: A 110 GLU cc_start: 0.8413 (mm-30) cc_final: 0.8104 (mm-30) REVERT: A 266 MET cc_start: 0.8500 (OUTLIER) cc_final: 0.7959 (ptt) REVERT: A 590 GLU cc_start: 0.8170 (mm-30) cc_final: 0.7948 (mm-30) REVERT: B 266 MET cc_start: 0.8485 (OUTLIER) cc_final: 0.8145 (ptt) REVERT: C 266 MET cc_start: 0.8549 (OUTLIER) cc_final: 0.8135 (ptt) REVERT: C 626 ILE cc_start: 0.8003 (pt) cc_final: 0.7708 (mp) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.0794 time to fit residues: 7.1332 Evaluate side-chains 54 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 46 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 142 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 89 optimal weight: 0.8980 chunk 123 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 76 optimal weight: 0.5980 chunk 138 optimal weight: 4.9990 chunk 103 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.111123 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.088191 restraints weight = 19137.837| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 2.56 r_work: 0.2936 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2936 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 11902 Z= 0.190 Angle : 0.565 12.876 16213 Z= 0.279 Chirality : 0.045 0.263 1836 Planarity : 0.004 0.040 2043 Dihedral : 5.241 44.270 2061 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.26 % Allowed : 7.55 % Favored : 91.19 % 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: 0.22 (0.22), residues: 1437 helix: 1.82 (0.27), residues: 381 sheet: -0.80 (0.32), residues: 243 loop : -0.31 (0.21), residues: 813 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.020 0.002 TYR A 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 585 HIS 0.006 0.001 HIS B 18 Details of bonding type rmsd covalent geometry : bond 0.00449 (11860) covalent geometry : angle 0.51413 (16105) SS BOND : bond 0.00318 ( 18) SS BOND : angle 1.25829 ( 36) hydrogen bonds : bond 0.03962 ( 468) hydrogen bonds : angle 4.92597 ( 1368) link_BETA1-4 : bond 0.00297 ( 6) link_BETA1-4 : angle 1.18428 ( 18) link_NAG-ASN : bond 0.00823 ( 18) link_NAG-ASN : angle 3.92030 ( 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 59 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.381 Fit side-chains REVERT: A 110 GLU cc_start: 0.8428 (mm-30) cc_final: 0.8109 (mm-30) REVERT: A 266 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.7979 (ptt) REVERT: A 590 GLU cc_start: 0.8174 (mm-30) cc_final: 0.7914 (mm-30) REVERT: B 266 MET cc_start: 0.8501 (OUTLIER) cc_final: 0.8167 (ptt) REVERT: C 266 MET cc_start: 0.8550 (OUTLIER) cc_final: 0.8126 (ptt) REVERT: C 626 ILE cc_start: 0.8013 (pt) cc_final: 0.7696 (mp) outliers start: 15 outliers final: 9 residues processed: 53 average time/residue: 0.0735 time to fit residues: 6.8038 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 : 0.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR Chi-restraints excluded: chain A residue 57 VAL 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 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 57 VAL 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: 0.9990 chunk 27 optimal weight: 3.9990 chunk 124 optimal weight: 0.6980 chunk 9 optimal weight: 1.9990 chunk 89 optimal weight: 0.7980 chunk 80 optimal weight: 2.9990 chunk 92 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 64 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.112315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.089358 restraints weight = 19416.202| |-----------------------------------------------------------------------------| r_work (start): 0.3114 rms_B_bonded: 2.55 r_work: 0.2959 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.3595 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= 0.147 Angle : 0.533 12.790 16213 Z= 0.263 Chirality : 0.044 0.255 1836 Planarity : 0.004 0.038 2043 Dihedral : 5.122 45.846 2061 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.76 % Allowed : 7.89 % 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: 0.34 (0.22), residues: 1437 helix: 2.04 (0.27), residues: 375 sheet: -1.06 (0.34), residues: 213 loop : -0.21 (0.20), residues: 849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 112 TYR 0.020 0.001 TYR A 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 585 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00343 (11860) covalent geometry : angle 0.48084 (16105) SS BOND : bond 0.00272 ( 18) SS BOND : angle 1.13995 ( 36) hydrogen bonds : bond 0.03796 ( 468) hydrogen bonds : angle 4.80592 ( 1368) link_BETA1-4 : bond 0.00339 ( 6) link_BETA1-4 : angle 1.07754 ( 18) link_NAG-ASN : bond 0.00813 ( 18) link_NAG-ASN : angle 3.86588 ( 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 59 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.441 Fit side-chains REVERT: A 110 GLU cc_start: 0.8377 (mm-30) cc_final: 0.8067 (mm-30) REVERT: A 266 MET cc_start: 0.8424 (OUTLIER) cc_final: 0.7938 (ptt) REVERT: A 590 GLU cc_start: 0.8136 (mm-30) cc_final: 0.7891 (mm-30) REVERT: B 266 MET cc_start: 0.8542 (OUTLIER) cc_final: 0.8126 (ptt) REVERT: C 57 VAL cc_start: 0.8579 (OUTLIER) cc_final: 0.8369 (m) REVERT: C 266 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8094 (ptt) outliers start: 9 outliers final: 3 residues processed: 53 average time/residue: 0.0883 time to fit residues: 7.7516 Evaluate side-chains 55 residues out of total 1275 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 25 THR 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 57 VAL 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: 3.9990 chunk 96 optimal weight: 10.0000 chunk 109 optimal weight: 0.9990 chunk 121 optimal weight: 0.0570 chunk 142 optimal weight: 4.9990 chunk 84 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 105 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.089528 restraints weight = 19150.614| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.54 r_work: 0.2963 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2963 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.3640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11902 Z= 0.140 Angle : 0.535 12.769 16213 Z= 0.264 Chirality : 0.044 0.255 1836 Planarity : 0.003 0.037 2043 Dihedral : 5.050 46.571 2061 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 0.76 % Allowed : 8.05 % Favored : 91.19 % 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: 2.18 (0.27), residues: 372 sheet: -1.07 (0.34), residues: 213 loop : -0.22 (0.20), residues: 852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 112 TYR 0.019 0.001 TYR A 650 PHE 0.008 0.001 PHE A 121 TRP 0.005 0.001 TRP B 514 HIS 0.005 0.001 HIS C 18 Details of bonding type rmsd covalent geometry : bond 0.00327 (11860) covalent geometry : angle 0.48460 (16105) SS BOND : bond 0.00250 ( 18) SS BOND : angle 0.96404 ( 36) hydrogen bonds : bond 0.03752 ( 468) hydrogen bonds : angle 4.76510 ( 1368) link_BETA1-4 : bond 0.00323 ( 6) link_BETA1-4 : angle 1.10547 ( 18) link_NAG-ASN : bond 0.00818 ( 18) link_NAG-ASN : angle 3.84843 ( 54) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2084.20 seconds wall clock time: 36 minutes 52.63 seconds (2212.63 seconds total)